{"help": "https://data.iadb.org/es/api/3/action/help_show?name=datastore_search", "success": true, "result": {"include_total": false, "limit": 100, "records_format": "objects", "resource_id": "456876d5-a54d-4fe6-8680-1aeb5ac691e4", "total_estimation_threshold": null, "last_id_operator": "gt", "records": [{"_id":1,"Tool_Name":"Pubmed","ID":"1","Main_URL":"https://pubmed.ncbi.nlm.nih.gov/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the database as part of the Entrez system of information retrieval.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Sistemas Bioinformaticos,Diplomado en Bioinformática,Access Bioinformatics Databases with Biopython","Notes":null,"Year_Published":"1996","Country_or_Region":"USA"},{"_id":2,"Tool_Name":"Web Of Science","ID":"2","Main_URL":"https://mjl.clarivate.com/home","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Web of Science is a website which provides subscription-based access to multiple databases that provide comprehensive citation data for many different academic disciplines. It was originally produced by the Institute for Scientific Information (ISI) and is currently maintained by Clarivate Analytics (previously the Intellectual Property and Science business of Thomson Reuters).","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"1997","Country_or_Region":"USA"},{"_id":3,"Tool_Name":"Scopus","ID":"3","Main_URL":"https://www.scopus.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Scopus is Elsevier’s abstract and citation database launched in 2004. Scopus covers nearly 36,377 titles (22,794 active titles and 13,583 inactive titles) from approximately 11,678 publishers, of which 34,346 are peer-reviewed journals in top-level subject fields: life sciences, social sciences, physical sciences and health sciences. It covers three types of sources: book series, journals, and trade journals. All journals covered in the Scopus database, regardless of who they are published under, are reviewed each year to ensure high quality standards are maintained. Searches in Scopus also incorporate searches of patent databases.[1] Scopus gives four types of quality measure for each title; those are h-Index, CiteScore, SJR (SCImago Journal Rank) and SNIP (Source Normalized Impact per Paper).","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2004","Country_or_Region":"Netherlands"},{"_id":4,"Tool_Name":"Google Scholar","ID":"4","Main_URL":"https://scholar.google.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Google Scholar is a freely accessible web search engine that indexes the full text or metadata of scholarly literature across an array of publishing formats and disciplines. Released in beta in November 2004, the Google Scholar index includes most peer-reviewed online academic journals and books, conference papers, theses and dissertations, preprints, abstracts, technical reports, and other scholarly literature, including court opinions and patents. While Google does not publish the size of Google Scholar's database, scientometric researchers estimated it to contain roughly 389 million documents including articles, citations and patents making it the world's largest academic search engine in January 2018. An statistical estimate published in PLOS ONE using a Mark and recapture method estimated approximately 80–90% coverage of all articles published in English with an estimate of 100 million. This estimate also determined how many documents were freely available on the web.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2004","Country_or_Region":"USA"},{"_id":5,"Tool_Name":"Directory of Open Access Journals (DOAJ)","ID":"5","Main_URL":"https://doaj.org/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"The Directory of Open Access Journals (DOAJ) is a website that hosts a community-curated list of open access journals, maintained by Infrastructure Services for Open Access (IS4OA). The project defines open access journals as scientific and scholarly journals making all their content available for free, without delay or user-registration requirement, and meeting high quality standards, notably by exercising peer review or editorial quality control. DOAJ uses the Budapest Open Access Initiative's definition of open access to define required rights given to users, for the journal to be included, as the rights to \"read, download, copy, distribute, print, search, or link to the full texts of [the] articles, or use them for any other lawful purpose\". The mission of DOAJ is to \"increase the visibility, accessibility, reputation, usage and impact of quality, peer-reviewed, open access scholarly research journals\".\nIn August 2020, the independent database contains more than 15,060 open access journals and 5,215,227 articles covering all areas of science, technology, medicine, social sciences and the humanities.\n15,250 Journals\n12,226 searchable at Article level\n134 Countries\n5,302,660 Articles","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Diplomado en Bioinformática","Notes":null,"Year_Published":"2003","Country_or_Region":null},{"_id":6,"Tool_Name":"PLOS","ID":"6","Main_URL":"https://plos.org/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"PLOS is a nonprofit, Open Access publisher empowering researchers to accelerate progress in science and medicine by leading a transformation in research communication.\nFEATURED COMMUNITIES: Molecular Biology, Ecology, Immunology, Microbiology, Neuroscience,  Cancer treatment and research.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2003","Country_or_Region":"USA"},{"_id":7,"Tool_Name":"Sci-Hub","ID":"7","Main_URL":"https://sci-hub.tw/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Sci-Hub is a shadow library website that provides free access to millions of research papers and books, without regard to copyright, by bypassing publishers' paywalls in various ways. Sci-Hub was founded by Alexandra Elbakyan in 2011 in Kazakhstan in response to the high cost of research papers behind paywalls. The site is extensively used worldwide. In September 2019, the site's owners said that it served approximately 400,000 requests per day. The number of articles claimed is frequently updated on the site's home page, being over 81 million in April 2020.\nIn June 2020, a study found that articles downloaded from Sci-Hub were cited 1.72 times more than papers not downloaded from Sci-Hub.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2011","Country_or_Region":"Russia"},{"_id":8,"Tool_Name":"Google Patents","ID":"8","Main_URL":"https://patents.google.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Indexes more than 87 million patents with full text from the patent offices of 17 different countries, including:\n- United States Patent and Trademark Office (USPTO)\n- European Patent Office (EPO)\n- China’s National Intellectual Property Administration (CNIPA)\n- Japan Patent Office (JPO)\n- Korean Intellectual Property Office (KIPO)\n- World Intellectual Property Organization (WIPO)\n- Deutsches Patent- und Markenamt (DPMA)\n- Canadian Intellectual Property Office (CIPO)\n- And patent data from various other patent offices of countries including Russia, UK, France, Spain, Belgium, Denmark, Finland, Luxembourg, and the Netherlands.\n\nGoogle Patents allows to search patents on the basis of the following variables:\n- Search terms\n- Date\n- Assignee\n- Inventor\n\nThis can be further classified with the following filters –\n- Patent Office\n- Status (granted/applied)\n- Type (patent/design)","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2006","Country_or_Region":"USA"},{"_id":9,"Tool_Name":"Espacenet","ID":"9","Main_URL":"https://worldwide.espacenet.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Born out of a collaboration between the European Patent Office (EPO) and the European Patent Organization.\nOffers patents from 97 countries with a database of more than 120 million patents (november 2020). The website uses an excellent machine translation system which is one of the most efficient patent translators. \n\nYou can search for patents on Espacenet by opting for either of the options below:\n--- Smart search: In smart search, you can enter up to 20 search terms (a maximum of ten terms per searchable bibliographic data), with or without field identifiers.\n--- Advanced search: In advanced search, you can perform an in-depth search with the following variables/categories:\n- Title\n- Abstract\n- Publication number\n- Application number\n- Priority number\n- Publication date\n- Applicants\n- Inventor(s)\n- CPC\n- IPC\n--- Classification Search: In this section, you can search for patents on the basis of CPC (Cooperative Patent Classification).","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"1998","Country_or_Region":"Europe"},{"_id":10,"Tool_Name":"USPTO Web Patent Database","ID":"10","Main_URL":"https://assignment.uspto.gov/patent/index.html#/patent/search","Usage":"Repository and DB","Biotech_Fields":"All","Description":"USPTO is the federal agency of the United States Government responsible for grants of U.S. patents and registration of trademarks.\nThe website shows published and applied patents,  and also gives information on what patents are, elegibility, patent application process, patent maintenance, etc.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":"https://www.greyb.com/patent-search/#US-Patent-Search","Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":11,"Tool_Name":"Patentscope - WIPO","ID":"11","Main_URL":"https://patentscope.wipo.int/search/en/search.jsf","Usage":"Repository and DB","Biotech_Fields":"All","Description":"WIPO is the world intellectual property organization and includes 192 member states.  \nIncludes over 92 million patent documents including 3.9 million published international patent applications (PCT).\nSearch options:\n- quick search\n- advanced search","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"Data coverage: https://patentscope.wipo.int/search/en/help/data_coverage.jsf","Learning _Resources":"WIPO eLearning Center","Notes":null,"Year_Published":"1967","Country_or_Region":"International"},{"_id":12,"Tool_Name":"Lens","ID":"12","Main_URL":"https://www.lens.org/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Lens.org is an open-source patent database. It is an initiative of Cambia and Queensland University of Technology. Started in 2000, the database currently displays over 119 Million documents from 105 jurisdictions. Allows for document collections, aggregations, and analyses to be shared, annotated, and embedded to forge open mapping of the world of knowledge-directed innovation. Is one of the few databases on which you can search by gene sequences.\n\n--- The various patent data sources ingested and integrated in the Lens:\nThe European Patent Office’s DocDB bibliographic data from 1907 - present: 81+ Million documents from nearly 100 jurisdictions.\nUSPTO Applications from 2001 – present with full text and images.\nUSPTO Grants from 1976 – present with full text and images.\nUSPTO Assignments (14+ Million).\nEuropean Patent Office (EP) Grants from 1980 – present with full text and images.\nWIPO PCT Applications from 1978 – present with full text and images.\nAustralian Patent Full Text from IP Australia\n\n--- You can conduct searches on the basis of following-\nNumerous Variables\nFull-Text\nTitle\nAbstract\nInventor\nApplicant/Assignee\nPublication Number\nFiling Number\n\n--- And you can apply the following filter on your patent searches\nFlags\nInstitution\nInstitution Country/Region\nAuthor\nIdentifier Type\nFunding\nJournal\nConference Name\nPublication Type\nPublisher\nSubject Matter\nOpen Access\nQuery Tools\nNew Structured Search\nPublishing Year\n\nYou can also search for lapsed, abandoned, or expired US patents via the INPADOC patent status and family information service. Patent families may be visualized using graphical trees as PDFs.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2000","Country_or_Region":"Australia"},{"_id":13,"Tool_Name":"Derwent World Patents Index","ID":"13","Main_URL":"https://clarivate.com/derwent/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"The Derwent World Patents Index of Clarivate Analytics is a patent database with large coverage, including documents from 44 patent issuing authorities across the world. It provides an option to read the summary of patents in a non-legal language i.e. in a simple technical language.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Other pricing model","Pricing_Detail":"Variable pricing depending on modules used and usage.","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":null},{"_id":14,"Tool_Name":"PatBase","ID":"14","Main_URL":"https://www.patbase.com/login.asp","Usage":"Repository and DB","Biotech_Fields":"All","Description":"PatBase is a patent database that contains 66 million full-text documents from over 105 authorities worldwide, including Israel. Allows to conduct a citation search on it.\nPatBase is a primary search tool used to search, review, share and analyse businesscritical patent information. PatBase is a global patent database covering over 100 authorities. The database hosts 111+ million patent and related documents organised into 57+ million patent families.\nPatBase Analytics is fully integrated into PatBase. Users can analyse patent data from up to 100,000 families at once, directly from their search results. Patent data can be visualised through detailed and transparent graphs to understand the landscape.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Subscription only","Pricing_Detail":"The most basic account PatBase Express is available for  US$4000/year or US$2000Yyear for academic use.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://minesoft.com/our-products/patbase/\nFind out more about PatBase at: www.minesoft.com/our-products/patbase/\nFind out more about PatBase Express at: www.minesoft.com/our-products/patbaseexpress/","Learning _Resources":null,"Notes":null,"Year_Published":"1996","Country_or_Region":"UK"},{"_id":15,"Tool_Name":"PatSeer","ID":"15","Main_URL":"https://patseer.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Patseer is a patent database that holds 61+ million full-text records from 43 patent offices. Here is possible to lookup Corporate Trees of Top 5000 companies.\nSearch variables like: assignee name, inventor name, search history, saved searches, chemical synonym lookup, IPC/US/CPC classification definition search, term index lookup, multi-language translator, and number converter wizard. \n---> As well as conducting searches using the following variables:\nProximity\ncomplex Boolean with proximity\ncommand-line searching\nSearch Scripting\nWildcards\nleft & middle truncation\nhit count cutoff\nNatural Language Search Aids  \nNormalized Assignee Names  \n\nAfter the search, you can analyze search results via multi-dimensional charts such as column, line, pie, area, bubble, heatmap, and geographical map.\n\n136,494,967+ TOTAL RECORDS. 106+ NUMBER OF PATENT AUTHORITES available.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Subscription only","Pricing_Detail":"Subscriptions start from US$900 Per User/Per Quarter","Documentation_and_Tutorials":null,"Alternative_URLs":"https://patseer.com/pricing/","Learning _Resources":null,"Notes":null,"Year_Published":"2012","Country_or_Region":"India"},{"_id":16,"Tool_Name":"Drug Patent Watch","ID":"16","Main_URL":"https://www.drugpatentwatch.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Drug Patent Watch is a patent database that keeps track of drug patents from 134 countries.\n\n--- For launching a drug in the market, Drug Patent Watch lets you:\nAssess market potential through historic sales figures\nAlign distribution methods with information on where and how drugs are purchased\nAssess levels of generic competition\nUse drug price ranges to evaluate price elasticity\nDetermine optimal prices before launch\nConduct landscape analysis, track drug development, explore new indications for existing drugs, anticipate 505(b)(2) approval, and track OTC-switches, new formulations, and other drug improvements.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Subscription only","Pricing_Detail":"Subscriptions start from US$4,200/month","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2002","Country_or_Region":"USA"},{"_id":17,"Tool_Name":"Patsnap","ID":"17","Main_URL":"https://www.patsnap.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Patsnap is a patent database from more than 40 countries. Considered an ideal database for landscape analysis, getting insights, and analytics data.\n\n--- Search options:\nSimple\nBulk\nAdvanced\nSemantic\nExpand\nClassified\nLegal\nImage\nChemical\nLiterature","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Other pricing model","Pricing_Detail":"Starts from US$75/month.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/patsnap","Learning _Resources":"How to use innovation intelligence to evaluate a competitive landscape,Types of IP and Strategy,Intellectual Property in Life Sciences,Intellectual Property for R&D,Patent and IP Basics,On-deman Webinars about IP","Notes":null,"Year_Published":"2007","Country_or_Region":"Singapore"},{"_id":18,"Tool_Name":"NCBI","ID":"18","Main_URL":"https://www.ncbi.nlm.nih.gov/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information. Supported by the NIH in USA. \nHost of one of the largest primary database for genomic information and related tools.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Sistemas Bioinformaticos,The Biostar Handbook,Applied Bioinformatics (2020),Learn Bioinformatics the Right Way (2019),Bioinformatics Recipes,Bioinformatics Specialization,Bioinformatics: Introduction and Methods,Biology Meets Programming: Bioinformatics for Beginners,Whole genome sequencing of bacterial genomes - tools and applications,Case Studies in Functional Genomics,Variant Analysis,Diplomado en Bioinformática,Foundations of Computational and Systems Biology,Genomics and the Other Omics: The Comprehensive Essentials,Access Bioinformatics Databases with Biopython,NCBI Mastery- A Beginner's Guide to Bioinformatics","Notes":null,"Year_Published":"1988","Country_or_Region":"USA"},{"_id":19,"Tool_Name":"NCBI - BLAST","ID":"19","Main_URL":"https://blast.ncbi.nlm.nih.gov/Blast.cgi","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"BLAST is a sequence alignment and search tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.\nThis platform uses the NCBI database and allows 4 possible alignments using its search tool: \n- Nucleotide Blast: nucleotide > nucleotide\n- BlastX: nucleotide > protein\n- TBlastN: protein > nucleotide\n- Protein Blast: protein > protein","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Bioinformática para Principiantes,Sistemas Bioinformaticos,The Biostar Handbook,Applied Bioinformatics (2020),Learn Bioinformatics the Right Way (2019),Bioinformatics Recipes,Bioinformatics Specialization,Bioinformatics: Introduction and Methods,Biology Meets Programming: Bioinformatics for Beginners,Whole genome sequencing of bacterial genomes - tools and applications,Case Studies in Functional Genomics,Introduction to Python for Biologists,Advanced Python for Biologists,Data Manipulation and Visualisation with Python,BLAST and multiple sequence alignment (MSA) programs,Diplomado en Bioinformática,Foundations of Computational and Systems Biology,NCBI Mastery- A Beginner's Guide to Bioinformatics","Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":20,"Tool_Name":"NCBI - GenBank","ID":"20","Main_URL":"https://www.ncbi.nlm.nih.gov/genbank/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"Repository of DNA and RNA.\nGenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Bioinformática para Principiantes,Sistemas Bioinformaticos,The Biostar Handbook,Applied Bioinformatics (2020),Learn Bioinformatics the Right Way (2019),Bioinformatics Recipes,Bioinformatics Specialization,Bioinformatics: Introduction and Methods,Biology Meets Programming: Bioinformatics for Beginners,Whole genome sequencing of bacterial genomes - tools and applications,Case Studies in Functional Genomics,Variant Analysis,Diplomado en Bioinformática,Access Bioinformatics Databases with Biopython,NCBI Mastery- A Beginner's Guide to Bioinformatics","Notes":null,"Year_Published":"2013","Country_or_Region":"USA"},{"_id":21,"Tool_Name":"EMBL-EBI","ID":"21","Main_URL":"https://www.ebi.ac.uk/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Primary Database for biological information, including genomic, proteomic or chemical data. \nPart of the European Molecular Biology Laboratory (EMBL), and supported by the European Commission, between others.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Bioinformática para Principiantes,Sistemas Bioinformaticos,The Biostar Handbook,Applied Bioinformatics (2020),Learn Bioinformatics the Right Way (2019),Bioinformatics Recipes,Bioinformatics Specialization,Bioinformatics: Introduction and Methods,Biology Meets Programming: Bioinformatics for Beginners,Whole genome sequencing of bacterial genomes - tools and applications,Case Studies in Functional Genomics,Variant Analysis,Structural bioinformatics,A guide to identifying and prioritising drug targets with the Open Targets Platform,Mathematics of life: Modelling molecular mechanisms,>> Bioinformatics for Principal Investigators,Systems biology: From large datasets to biological insight,Summer school in bioinformatics,Proteomics bioinformatics,Curso Internacional: Estrategias bioinformáticas para el estudio de enfermedades tropicales desatendidas (ETDs),Microscopy data analysis: Machine learning and the BioImage Archive,Bioinformatics for Immunologists,Metagenomics bioinformatics,Bringing data to life - Data management for the biomolecular sciences,\"EMBL-EBI, programmatically\",Cancer genomics,Open Virtual Ensembl Browser Workshop,Introductory bioinformatics pathway,ResOps - Cloud-native tools and technology for researchers,Next Generation Sequencing Bioinformatics,Foundations of Computational and Systems Biology,NCBI Mastery- A Beginner's Guide to Bioinformatics","Notes":null,"Year_Published":null,"Country_or_Region":"UK"},{"_id":22,"Tool_Name":"EMBL-EBI - The European Nucleotide Archive (ENA)","ID":"22","Main_URL":"https://www.ebi.ac.uk/ena/browser/home","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Sistemas Bioinformaticos,The Biostar Handbook,Applied Bioinformatics (2020),Learn Bioinformatics the Right Way (2019),Bioinformatics Recipes,Bioinformatics Specialization,Bioinformatics: Introduction and Methods,Biology Meets Programming: Bioinformatics for Beginners,Whole genome sequencing of bacterial genomes - 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Data management for the biomolecular sciences","Notes":null,"Year_Published":null,"Country_or_Region":"UK"},{"_id":24,"Tool_Name":"Expasy - SIB Swiss Institute of Bioinformatics","ID":"24","Main_URL":"https://www.expasy.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics (more about its history).\nIt is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Sistemas Bioinformaticos,BLAST and multiple sequence alignment (MSA) programs,Phylogenetics of animal viral pathogens,High Performance Computing (HPC) in Life Sciences,\"NGS - Quality control, Alignment, Visualisation\",Introduction to Glycoinformatics,Galaxy introduction for life scientists,Protein sequence databases and sequence annotation at UniProtKB,Intermediate Python","Notes":null,"Year_Published":"1993","Country_or_Region":"Switzerland"},{"_id":25,"Tool_Name":"DNA Databank of Japan (DDBJ)","ID":"25","Main_URL":"https://www.ddbj.nig.ac.jp/index-e.html","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"DNA Databank of Japan Free resource. DDBJ Center collects nucleotide sequence data as a member of INSDC (International Nucleotide Sequence Database Collaboration) and provides freely available nucleotide sequence data and supercomputer system, to support research activities in life science.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Bioinformatics Specialization,Bioinformatics: Introduction and Methods,Biology Meets Programming: Bioinformatics for Beginners,Whole genome sequencing of bacterial genomes - tools and applications,Case Studies in Functional Genomics","Notes":null,"Year_Published":null,"Country_or_Region":"Japan"},{"_id":26,"Tool_Name":"Ensembl Genome Database","ID":"26","Main_URL":"http://www.ensembl.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Biomedicine","Description":"Ensembl genome database project is a scientific project at the European Bioinformatics Institute (EBI), which was launched in 1999 in response to the imminent completion of the Human Genome Project. Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.\nSimilar databases and browsers are found at NCBI and the University of California, Santa Cruz (UCSC).","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"1999","Country_or_Region":"Europe"},{"_id":27,"Tool_Name":"UC Santa Cruz - Genome","ID":"27","Main_URL":"http://genome.ucsc.edu/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Biomedicine","Description":"The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website.\nOn June 22, 2000, UCSC and the other members of the International Human Genome Project consortium completed the first working draft of the human genome assembly, forever ensuring free public access to the genome and the information it contains. A few weeks later, on July 7, 2000, the newly assembled genome was released on the web at http://genome.ucsc.edu, along with the initial prototype of a graphical viewing tool, the UCSC Genome Browser. In the ensuing years, the website has grown to include a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Genomics and the Other Omics: The Comprehensive Essentials,NCBI Mastery- A Beginner's Guide to Bioinformatics","Notes":null,"Year_Published":"2000","Country_or_Region":"USA"},{"_id":28,"Tool_Name":"Clustal + MUSCLE + MAFFT","ID":"28","Main_URL":"http://www.clustal.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology","Description":"Online tool series for Multiple alignment of nucleic acid and protein sequences.\n- ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. For the alignment of two sequences please instead use our pairwise sequence alignment tools. --> Has been retired. In replacement MUSCLE or MAFFT are recommended for nucleic acid sequences and CLUSTAL Omega for protein sequences.\n- Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. (*This tool can align up to 4000 sequences or a maximum file size of 4 MB.)\n- MUSCLE: MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options. (*This tool can align up to 500 sequences or a maximum file size of 1 MB.)\n- MAFFT: MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. (*This tool can align up to 500 sequences or a maximum file size of 1 MB.)\n\nServer options and downloads are available. \nPart of the EMBL-EBI suit of web-server softwares.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":"https://www.drive5.com/muscle/manual/\nhttps://www.ebi.ac.uk/seqdb/confluence/display/THD","Alternative_URLs":"https://www.ebi.ac.uk/Tools/msa/clustalo/ https://www.ebi.ac.uk/Tools/msa/muscle/ https://www.ebi.ac.uk/Tools/msa/mafft/ http://www.drive5.com/muscle/","Learning _Resources":"Sistemas Bioinformaticos,The Biostar Handbook,Applied Bioinformatics (2020),Learn Bioinformatics the Right Way (2019),Bioinformatics Recipes,Structural bioinformatics,Foundations of Computational and Systems Biology","Notes":null,"Year_Published":"1988","Country_or_Region":"Ireland"},{"_id":29,"Tool_Name":"UniProt","ID":"29","Main_URL":"https://www.uniprot.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"The Universal Protein Resource (UniProt) is primary database for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium is supported by 3 main institutions: EMBL-EBI, SIB and PIR.\nUniProt is comprised of four components, each optimised for different uses:\n1) The  UniProt Knowledgebase (UniProtKB)  is the central access point for extensive curated protein information, including function, classification, and cross-reference. UniProtKB comprises two sections: \n- UniProtKB/Swiss-Prot  which is manually annotated and is reviewed and\n- UniProtKB/TrEMBL  which is automatically annotated and is not reviewed.\n2) The  UniProt Reference Clusters (UniRef)  databases provide clustered sets of sequences from the UniProtKB and selected UniProt Archive records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences.\n3) The  UniProt Archive (UniParc)  is a comprehensive repository, used to keep track of sequences and their identifiers.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Sistemas Bioinformaticos,Structural bioinformatics,Bringing data to life - Data management for the biomolecular sciences,Introduction to Glycoinformatics,Protein sequence databases and sequence annotation at UniProtKB,Diplomado en Bioinformática","Notes":null,"Year_Published":"2002","Country_or_Region":"UK,Switzerland,USA"},{"_id":30,"Tool_Name":"PIR: Protein Information Resource","ID":"30","Main_URL":"https://proteininformationresource.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Primary database for protein information. Today is part of the UniProt Database. \nThe Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies (Wu et al., 2003).\nPIR was established in 1984 by the National Biomedical Research Foundation (NBRF) as a resource to assist researchers in the identification and interpretation of protein sequence information. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"1984","Country_or_Region":"USA"},{"_id":31,"Tool_Name":"Protein Data Bank (PDB)","ID":"31","Main_URL":"https://www.rcsb.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Primary Database for Protein 3D Structural information. \nThe Protein Data Bank (PDB) was established as the 1st open access digital data resource in all of biology and medicine. It is today a leading global resource for experimental data central to scientific discovery. Through an internet information portal and downloadable data archive, the PDB provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA).\n169117 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Structural bioinformatics,Introduction to Protein Structure Analysis,Foundations of Computational and Systems Biology,Computation for Biological Engineers,NCBI Mastery- A Beginner's Guide to Bioinformatics,Drug Design and Molecular Docking by using computation Tools","Notes":null,"Year_Published":"1971","Country_or_Region":"USA"},{"_id":32,"Tool_Name":"Interpro","ID":"32","Main_URL":"http://www.ebi.ac.uk/interpro/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Secondary Database for protein information. \nInterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 to amalgamate the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIR SuperFamily and, the structure-based SUPERFAMILY have been manually integrated and are available in InterPro for text- and sequence-based searching.\nInterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium. Combines protein signatures from these member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/207","Learning _Resources":"Structural bioinformatics,Metagenomics bioinformatics","Notes":null,"Year_Published":"1999","Country_or_Region":"UK"},{"_id":33,"Tool_Name":"PRINTS","ID":"33","Main_URL":"http://130.88.97.239/PRINTS/index.php","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Secondary Database for protein fingerprints. \nThe PRINTS database houses a collection of protein family fingerprints. These may be used to make familial and tentative functional assignments for uncharacterised sequences. The June 2003 release (version 37.0) includes 1,850 fingerprints, encoding ~11,000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database specialises in the provisional of hierarchical classifications of protein superfamilies, allowing fine-grained diagnoses - as such, it provides the bulk of the hierarchical family annotation in InterPro. PRINTS also underpins the Blocks database from Seattle and eMOTIF resource from Stanford. It is available for BLAST, fingerprint and text searches.\nPRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/212","Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"UK"},{"_id":34,"Tool_Name":"PROSITE","ID":"34","Main_URL":"https://www.expasy.org/resources/prosite","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Secondary Database for protein information. \nPROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. This resource supports COVID-19 / SARS-CoV-2 research.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/215","Learning _Resources":null,"Notes":null,"Year_Published":"1989","Country_or_Region":"Switzerland"},{"_id":35,"Tool_Name":"ProTeus","ID":"35","Main_URL":"http://www.proteus.cs.huji.ac.il/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Secondary Database for protein information. \nProTeus (PROtein TErminUS) is a tool for identification of short linear signatures in protein termini.\nIt is based on a positional-based search method for revealing short significant signatures in termini of proteins. ProTeus, now includes over 1 Million protein sequences.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/732","Learning _Resources":null,"Notes":null,"Year_Published":"2005","Country_or_Region":"Israel"},{"_id":36,"Tool_Name":"Pfam","ID":"36","Main_URL":"http://pfam.xfam.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Secondary Database for protein information. \nThe Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).\nPfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgr.ki.se/Pfam/, and in the US at http://pfam.wustl.edu/. The web pages can give access to the alignments, trees, protein structure and other functional information for each family. The Pfam libraries of HMMs can be used locally to define domains in complete genomes. Pfam currently contains over 18.259 (as of May 2020) protein families and domains.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/210","Learning _Resources":"Structural bioinformatics","Notes":null,"Year_Published":null,"Country_or_Region":"UK"},{"_id":37,"Tool_Name":"ProDom","ID":"37","Main_URL":"http://prodom.prabi.fr/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Secondary Database for protein information. \nThe ProDom database contains protein domain families automatically generated from the SWISS-PROT and TrEMBL databases by sequence comparison. ProDom is built with the MKDOM2 program, based on recursive PSI-BLAST homology searches. Inside each family, sequences are aligned using the Multalin program. ProDom-CG is built from ProDom as an extraction of sequences derived from complete genomes. Families found in ProDom-CG are thus a subset of ProDom families. ProDom (release 2003.1) contains 144,444 domain families containing two or more individual domains. ProDom can be searched on the World Wide Web to study domain arrangements for known protein families with the help of a user-friendly graphical interface. The ESPript program is used to generate publication quality alignments of ProDom families, including structural information. BLAST and SRS requests can also be performed, with links to several other protein or protein family databases (PDB, PROSITE, Pfam-A and InterPro). ProDom-SG is a ProDom-based server dedicated to the selection of candidate domains which could show new types of folds for structural genomics projects.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/214","Learning _Resources":null,"Notes":null,"Year_Published":"1996","Country_or_Region":"France"},{"_id":38,"Tool_Name":"SMART (Simple Modular Architecture Research Tool)","ID":"38","Main_URL":"http://smart.embl.de/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Proteomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry,Biophysics,Physiology,Neurobiology,Immunology,Pharmacology","Description":"Secondary Database for protein information. \nSMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the identification and annotation of protein domains and the analysis of domain architectures. The current release has added more than 200 original hand-curated domain models. This brings the total to more than 600 domain families represented among nuclear, signalling and extracellular proteins. Extensive annotation for each domain family is available, providing information on function, subcellular localization, phyletic distribution and tertiary structure. Annotation now includes links to OMIM in cases where a human disease is associated with one or more mutations in a particular domain. A non-redundant sequence database is searched weekly for occurrences of SMART domains and several intrinsic features (transmembrane regions, coiled coils, signal peptides and internal repeats), and results are stored in a relational database. We have included new analysis methods and updated others. Internal protein repeats and transmembrane regions are detected using Prospero and TMHMM2, respectively. Improvements in the web interface now allow easy searches for proteins that contain user-defined combinations of domains or intrinsic features within a specified phyletic range. New advanced queries provide direct access to the SMART database using SQL, so users are no longer restricted to using simple AND-NOT logic. Protein lists are displayed or retrieved in FASTA format (with optional filtering for the domain of interest). Schematic representations of proteins use dynamically generated single images, which enables easy inclusion of SMART output in users' documents. SMART now provides multiple sequence alignments coloured by consensus, thereby highlighting patterns of residue conservation. SMART is now mirrored at http://smart.ox.ac.uk. SMART provides a unique combination of powerful and accurate analytical tools with simple visualization of results.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/218 http://www.pnas.org/cgi/content/full/95/11/5857","Learning _Resources":null,"Notes":null,"Year_Published":"1998","Country_or_Region":"Germany"},{"_id":39,"Tool_Name":"AU-RICH ELEMENT DATABASE","ID":"39","Main_URL":"https://brp.kfshrc.edu.sa/ared","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Molecular Biology","Description":"Secondary Database for mRNAs.\nARED-Plus: an updated and expanded database of AU-rich element-containing mRNAs and pre-mRNAs. *AREs are conserved sequence elements that were first discovered in the 3'UTR of mammalian transcripts.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.oxfordjournals.org/nar/database/summary/34","Learning _Resources":null,"Notes":null,"Year_Published":"2018","Country_or_Region":"Saudi Arabia"},{"_id":40,"Tool_Name":"Nucleic Acid Database Project (NDB)","ID":"40","Main_URL":"http://ndbserver.rutgers.edu/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Molecular Biology","Description":"The NDB is an open access platform that contains information about experimentally-determined nucleic acids and complex assemblies.\nNDB allows to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and learn about nucleic acids.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"NCBI Mastery- A Beginner's Guide to Bioinformatics","Notes":null,"Year_Published":"1992","Country_or_Region":"USA"},{"_id":41,"Tool_Name":"bioRxiv","ID":"41","Main_URL":"https://www.biorxiv.org/about-biorxiv","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Molecular Biology","Description":"BioRxiv (\"bio-archive\") is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":null},{"_id":42,"Tool_Name":"SILVA","ID":"42","Main_URL":"https://www.arb-silva.de/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology","Description":"SILVA rRNA database project: A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.\nSequencing the ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction and nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA databases has been accepted by researchers worldwide as their standard tool for large scale ribosomal RNA analysis. To provide high quality and comprehensive rRNA databases comprising Bacteria, Archaea and Eukarya the SILVA system was implemented in 2007. It is designed as an automatic software pipeline for sequence retrieval, quality assignment and the alignment of nucleic acid sequences based on the latest comprehensive ARB alignments.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://en.wikipedia.org/wiki/SILVA_ribosomal_RNA_database","Learning _Resources":"Sistemas Bioinformaticos","Notes":null,"Year_Published":"2007","Country_or_Region":"Germany"},{"_id":43,"Tool_Name":"KEGG: Kyoto Encyclopedia of Genes and Genomes","ID":"43","Main_URL":"https://www.genome.jp/kegg/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology","Description":"KEGG: Kyoto Encyclopedia of Genes and Genomes\nKEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.\nIncludes related databases and softwares. \nKEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping tools, which enable understanding of cellular and organism-level functions from genome sequences and other molecular datasets. KEGG mapping is a predictive method of reconstructing molecular network systems from molecular building blocks based on the concept of functional orthologs. Since the introduction of the KEGG NETWORK database, various diseases have been associated with network variants, which are perturbed molecular networks caused by human gene variants, viruses, other pathogens and environmental factors. The network variation maps are created as aligned sets of related networks showing, for example, how different viruses inhibit or activate specific cellular signaling pathways. The KEGG pathway maps are now integrated with network variation maps in the NETWORK database, as well as with conserved functional units of KEGG modules and reaction modules in the MODULE database. The KO database for functional orthologs continues to be improved and virus KOs are being expanded for better understanding of virus-cell interactions and for enabling prediction of viral perturbations.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa970/5943834","Learning _Resources":"Sistemas Bioinformaticos,Diplomado en Bioinformática,Access Bioinformatics Databases with Biopython,NCBI Mastery- A Beginner's Guide to Bioinformatics","Notes":null,"Year_Published":"1995","Country_or_Region":"Japan"},{"_id":44,"Tool_Name":"Parts Registry iGEM","ID":"44","Main_URL":"http://parts.igem.org/Main_Page","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Microbiology,Biochemistry","Description":"Collection of genetic parts that are used in the assembly of biological systems and devices in synthetic biology.\nThe iGEM Parts Registry is a growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. As part of the synthetic biology community's efforts to make biology easier to engineer, it provides a source of genetic parts to iGEM teams and academic labs.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":"http://parts.igem.org/Help:FAQ","Alternative_URLs":"https://web.archive.org/web/20080507050954/http://partsregistry.org/Main_Page","Learning _Resources":"Sistemas Bioinformaticos","Notes":null,"Year_Published":"2012","Country_or_Region":"USA"},{"_id":45,"Tool_Name":"PubChem","ID":"45","Main_URL":"https://pubchem.ncbi.nlm.nih.gov/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Metabolomics,Molecular Biology,Biochemistry,Pharmacology,Chemistry","Description":"Primary Database for Chemical compounds. Part of the NCBI in USA. \nPubChem is the world's largest collection of freely accessible chemical information. Search chemicals by name, molecular formula, structure, and other identifiers. Find chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations and more.\nIncludes (november 2020): 111M Compounds, 287M Substances, 273M Bioactivities, 32M Literature, 25M Patents; from  760Data Sources.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Sistemas Bioinformaticos","Notes":null,"Year_Published":"2004","Country_or_Region":"USA"},{"_id":46,"Tool_Name":"BRENDA","ID":"46","Main_URL":"https://www.brenda-enzymes.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Proteomics,Metabolomics,Molecular Biology,Biochemistry,Pharmacology,Chemistry","Description":"BRENDA is the main collection of enzyme functional data available to the scientific community. It is available on-line for free at www.brenda-enzymes.org, and as an in-house database for commercial users.\nThe enzymes are classified according to the Enzyme Commission list of enzymes. Some 6500 \"different\" enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. The Handbook is not a compendium, the reader will have to go to the primary literature for more detailed information. Currently about 450 EC classes display a \"B\" in the 4th position of the EC number. A part of these enzymes is in the reviewing process of the enzyme commission of the IUBMB and awaiting their EC numbers. Another part is waiting for more data which are a prerequisite for being proposed to the IUBMB (e.g. a description of the purificatin procedure). Incompletely classified \"B-enzymes\" (preliminary BRENDA-supplied EC numbers) mostly fill gaps in otherwise established pathways.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://watermark.silverchair.com/gky1048.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAqEwggKdBgkqhkiG9w0BBwagggKOMIICigIBADCCAoMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTcJ-VxlFQyyfYbpyAgEQgIICVOn9nBdkGa5PzobdbewjALsZSKIIOuSbKNO9GOXHg8guydupDbd5tDSaATdOmvlU01E2jaZlgQe9CTA3wZKoMsCpDT81BvTE8pkBhKan0URHW-m60XHl3EMYZ_FrM6X_-wvh7sE4jOcUiXycap2n0o1wjvyp9GPiu_Szl-z_c2fBhX2Yd0wgYIaOUE2TfwVFKLIR3t2xaXBPqgmlcdUKJKEYaxaUtTi1UMusy-vESwI9zGkPQPbCilcsP3lJyo3JHS4ZufJiYZ1I7RisaahKpaMsLfwrMp76ds78nNZT2f8L7wjxDuy9FcZjM9eCMG1DzCRGKyBXh3mlcE_TFzt2JgMDIKkMRzw20kZlHvx1hCT3PoRw_Oc-1Z6XKnO-IfkjBqt6pPZpkN10gEkDPVc7A-p5hPmjwLKF5-wL5SlK8CBb4qMtihMqeLitdG2xhN_3Zk5BAnINTjkN_yKjyny4bYjU5LiZGZkET6XDmyI83X4Xld6Dew3-Zf7QzOXAD7sENb4zVIc9fXBho89aHQWk_pCtWibuqCTH436hW50ViSLCfJIFdU6UQhalH8JWXXKI4fh-pIPu5yJJirjfZSJyCJn2fEcQjUm7FOQgJTE1L-1jXBWc68oEgKB6aE5b2vhYH0SdSVzoE7pXGf_XnQzQaAgh8tlzmQ02JhU1Xf7BeXSNaAlDrvPxjWtDDCfphrqhvkRKT5DtR93OUeTEuFMhsbBMpFD54S4SBSVa3xvjmH3FsUGmIG3GJKe1Rltm2MzW02ohEpQynol6jz5z8oQLQvDzjmGQ","Learning _Resources":null,"Notes":null,"Year_Published":"2000","Country_or_Region":"Germany"},{"_id":47,"Tool_Name":"Influenza Research Database (IRD)","ID":"47","Main_URL":"https://www.fludb.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Transcriptomics,Proteomics,Molecular Biology,Microbiology,Immunology,Pharmacology,Epidemiology","Description":"Platform for Influenza surveillance.\nThe Influenza Research Database (IRD) is an integrative and comprehensive publicly available database and analysis resource to search, analyze, visualize, save and share data for influenza virus research. IRD is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services.\nThe platform allows to Search, Analyze and finally Save data in a personal workbench. \nContains avian and non-human mammalian influenza surveillance data, human clinical data associated with virus extracts, phenotypic characteristics of viruses isolated from extracts, and all genomic and proteomic data available in public repositories for influenza viruses. Links host surveillance and clinical data to sequence and phenotypic data for all well characterized influenza virus strains. Data obtained from public data sources for well characterized virus strains is supplemented with IRD generated data. The IRD will provide a suite of tools for analysis of all types of influenza data and a personal work bench on which each scientist can store lists of important data selected from that available on IRD. The foundation of IRD is the genomic and protein sequence and annotation information imported from GenBank and UniProt. Data are uploaded from these sources into IRD on a daily basis.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://en.wikipedia.org/wiki/Influenza_Research_Database https://onlinelibrary.wiley.com/doi/full/10.1111/j.1750-2659.2011.00331.x","Learning _Resources":null,"Notes":null,"Year_Published":"2011","Country_or_Region":"USA"},{"_id":48,"Tool_Name":"GISAID","ID":"48","Main_URL":"https://www.gisaid.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Transcriptomics,Proteomics,Molecular Biology,Microbiology,Immunology,Pharmacology,Epidemiology","Description":"GISAID is a global science initiative and primary source that provides open-access to genomic data of influenza viruses and the novel coronavirus responsible for COVID-19. Since its establishment in 2008, as an alternative to sharing avian influenza data via conventional public-domain archives, GISAID is recognized for incentivizing rapid exchange of outbreak data during the H1N1 pandemic in 2009, the H7N9 epidemic in 2013, and the COVID-19 pandemic in 2020. In 2020, GISAID entered into the global research effort to understand SARS-CoV-2, the virus responsible for the COVID-19 pandemic, by making available genomic sequences that are modeled in real time, thereby helping to detect viral mutations and track movement of the virus across the planet. Huge volumes of SARS-CoV-2 genome sequences have been added to the GISAID database, rapidly shared by laboratories around the world.\nAllows for fast and easy way to publish and search viralgenomic data. Maintains the authorship over the published sequences, certain uses of their sequences are subject to a direct permission request to the authors.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://en.wikipedia.org/wiki/GISAID","Learning _Resources":null,"Notes":null,"Year_Published":"2008","Country_or_Region":"Germany"},{"_id":49,"Tool_Name":"Nextstrain","ID":"49","Main_URL":"https://nextstrain.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Transcriptomics,Proteomics,Molecular Biology,Microbiology,Epidemiology","Description":"Platform for Real-time tracking of pathogen evolution. \nNextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response.\nIt allows to have an international look to make traceability of different pathogens at a global level. The tool allows you to make trees and see where the strains come from, as well as the evolution that different sequences have had in time. It can be used for viruses and bacteria. Is a visually easy-to-use tool, but is limited as an analysis tool.\nNextstrain consists of:\n- “Augur” — a series of composable, modular (Unix-like) bioinformatics tools. We use these to create recipes for different pathogens and different analyses, which are easy to reproduce when new data is available.\n- “Auspice” — a web-based visualization program, to present & interact with phylogenomic & phylogeographic data. This is what you see when, for example, you visit nextstrain.org/zika, but it can also run locally on your computer.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://github.com/nextstrain https://academic.oup.com/bioinformatics/article/34/23/4121/5001388","Learning _Resources":null,"Notes":null,"Year_Published":"2018","Country_or_Region":"USA,Switzerland"},{"_id":50,"Tool_Name":"HUGO Gene Nomenclature Comittee (HGNC)","ID":"50","Main_URL":"https://www.genenames.org/","Usage":"Repository and DB","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.\n\ngenenames.org is a curated online repository of HGNC-approved gene nomenclature, gene families and associated resources including links to genomic, proteomic and phenotypic information.\n\nGives access to a catalogue of more than 39,000 symbol reports, search lists of symbols using our Multi-symbol checker and identify possible orthologs using our HCOP tool.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"1978","Country_or_Region":"USA,Israel"},{"_id":51,"Tool_Name":"Mendeley","ID":"51","Main_URL":"https://www.mendeley.com/","Usage":"Other","Biotech_Fields":"All","Description":"Mendeley provides products and services for academic researchers. It is most known for its reference manager which is used to manage and share research papers and generate bibliographies for scholarly articles.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2008","Country_or_Region":"UK"},{"_id":52,"Tool_Name":"Mendeley Data","ID":"52","Main_URL":"https://data.mendeley.com/","Usage":"Data Storage","Biotech_Fields":"All","Description":"A free research data management solution from the Mendeley company.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"UK"},{"_id":53,"Tool_Name":"Endnote","ID":"53","Main_URL":"https://endnote.com/","Usage":"Other","Biotech_Fields":"All","Description":"EndNote is a commercial reference management software package, used to manage bibliographies and references when writing essays and articles. It is produced by Clarivate Analytics (previously by Thomson Reuters).","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic","Pricing_Model":"Freemiun","Pricing_Detail":"Free basic account. A one-time Upgrade License costs US$99.95, a Full License US$249.95, and a Student License US$115.95.","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"1995","Country_or_Region":"USA"},{"_id":54,"Tool_Name":"Matlab","ID":"54","Main_URL":"https://www.mathworks.com/products/matlab.html","Usage":"Data Analysis","Biotech_Fields":"All","Description":"MATLAB (an abbreviation of \"matrix laboratory\") is a proprietary multi-paradigm programming language and numerical computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.\nAlthough MATLAB is intended primarily for numerical computing, an optional toolbox uses the MuPAD symbolic engine allowing access to symbolic computing abilities. An additional package, Simulink, adds graphical multi-domain simulation and model-based design for dynamic and embedded systems.\nAs of 2020, MATLAB has more than 4 million users worldwide.","Technology_Type":"Programming Environment/Library","Level_of_Complexity":"Advanced","Pricing_Model":"Subscription only","Pricing_Detail":"USD 2,150 - Perpetual license\nUSD 860 - Annual license\nUSD 49 - Student license\nUSD 99 - Student suite license","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"An Introduction to MATLAB for biologists,Network Analysis in Systems Biology,SysMIC training in Computational Biology","Notes":null,"Year_Published":"1984","Country_or_Region":"USA"},{"_id":55,"Tool_Name":"R Studio","ID":"55","Main_URL":"https://rstudio.com/","Usage":"Data Analysis","Biotech_Fields":"All","Description":"RStudio is an integrated development environment (IDE) for R, a programming language for statistical computing and graphics. It is available in two formats: RStudio Desktop is a regular desktop application while RStudio Server runs on a remote server and allows accessing RStudio using a web browser.","Technology_Type":"Programming Environment/Library","Level_of_Complexity":"Advanced","Pricing_Model":"Freemiun","Pricing_Detail":"RStudio Desktop Pro: US$995/year/user\nRStudio Server Pro Standard: US$4,975/year with 5-users\nRStudio Server Pro Enterprise: US$11,950/year with 10 users","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Sistemas Bioinformaticos,\"Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R\",Case Studies in Functional Genomics,R for Biologists,RNA-seq Data Analysis,Systems biology: From large datasets to biological insight,Introduction to R,R Introduction tutorial,Diploma de Postítulo en Bioinformática y Biología Computacional,Diplomado en Bioinformática,Systems Biology and Biotechnology Specialization,Network Analysis in Systems Biology,Differential Gene Expression Analysis - Your Complete A to Z,Data Analysis for Life Sciences,SysMIC training in Computational Biology,Bioinformatics Industrial Certificate Program (BICP),Graficación para publicación de resultados de investigaciones científicas mediante el sistema R","Notes":null,"Year_Published":"2011","Country_or_Region":"USA"},{"_id":56,"Tool_Name":"Fiji","ID":"56","Main_URL":"https://fiji.sc/","Usage":"Data Analysis","Biotech_Fields":"All","Description":"Fiji is an open source image processing package based on ImageJ. Fiji's main purpose is to provide a distribution of ImageJ with many bundled plugins. Fiji features an integrated updating system and aims to provide users with a coherent menu structure, extensive documentation in the form of detailed algorithm descriptions and tutorials, and the ability to avoid the need to install multiple components from different sources.\nFiji is also targeted at developers, through the use of a version control system, an issue tracker, dedicated development channels, and a rapid-prototyping infrastructure in the form of a script editor which supports BeanShell, Jython, JRuby, and other scripting languages, as well as just-in-time Java development.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://imagej.net/ImageJ","Learning _Resources":null,"Notes":null,"Year_Published":"2007","Country_or_Region":"USA"},{"_id":57,"Tool_Name":"Copasi","ID":"57","Main_URL":"http://copasi.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Cell Biology,Molecular Biology,Biochemistry","Description":"COPASI: Software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations.\nCOPASI: (COmplex PAthway SImulator) is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Mathematics of life: Modelling molecular mechanisms","Notes":"*Current funding: National Institutes of Health (USA), grant GM080219 (NIGMS). BMBF Federal Ministry of Education (Germany).","Year_Published":"2004","Country_or_Region":"USA"},{"_id":58,"Tool_Name":"Jupyter","ID":"58","Main_URL":"https://jupyter.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Project Jupyter is a nonprofit organization created to \"develop open-source software, open-standards, and services for interactive computing across dozens of programming languages\". Spun off from IPython in 2014 by Fernando Pérez, Project Jupyter supports execution environments in several dozen languages. Project Jupyter has developed and supported the interactive computing products Jupyter Notebook, JupyterHub, and JupyterLab, the next-generation version of Jupyter Notebook. \nJupyter is language agnostic and it supports execution environments (aka kernels) in several dozen languages among which are Julia, R, Haskell, Ruby, and of course Python (via the IPython kernel).\n\n- Jupyter Notebook (formerly IPython Notebooks) is a web-based interactive computational environment for creating Jupyter notebook documents. The \"notebook\" term can colloquially make reference to many different entities, mainly the Jupyter web application, Jupyter Python web server, or Jupyter document format depending on context. A Jupyter Notebook document is a JSON document, following a versioned schema, and containing an ordered list of input/output cells which can contain code, text (using Markdown), mathematics, plots and rich media, usually ending with the \".ipynb\" extension. A Jupyter Notebook can be converted to a number of open standard output formats (HTML, presentation slides, LaTeX, PDF, ReStructuredText, Markdown, Python)\n- Jupyter kernel is a program responsible for handling various types of requests (code execution, code completions, inspection), and providing a reply. Kernels talk to the other components of Jupyter using ZeroMQ over the network, and thus can be on the same or remote machines.\n- JupyterHub is a multi-user server for Jupyter Notebooks. It is designed to support many users by spawning, managing, and proxying many singular Jupyter Notebook servers.\n- JupyterLab is the next-generation user interface for Project Jupyter. It offers all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface.\n- Jupyter Book is an open source project for building beautiful, publication-quality books and documents from computational material. This allows the user to construct the content in a mixture of Markdown an extended version of Markdown called MyST, Maths & Equations using MathJax, Jupyter Notebooks, reStructuredText, the output of running Jupyter Notebooks at build time, etc. Multiple output formats can be produced currently Single Files & Multipage HTML web pages and PDF files.","Technology_Type":"Programming Environment/Library","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://jupyter.org/about","Learning _Resources":"Bioinformática para Principiantes,Sistemas Bioinformaticos,Python Programming in 100 hours,Introduction to Python for Biologists,Advanced Python for Biologists,Data Manipulation and Visualisation with Python,Data Science for Everyone,Systems biology: From large datasets to biological insight,Linux y Bash/AWK scripting Boot Camp con aplicaciones en bioinformática,An Introduction to Solving Biological Problems with Python,\"NGS - Quality control, Alignment, Visualisation\",Intermediate Python,Diploma de Postítulo en Bioinformática y Biología Computacional,Computation for Biological Engineers,Bioinformatics with Python,DNA Research using Biopython,SysMIC training in Computational Biology","Notes":null,"Year_Published":"2015","Country_or_Region":"USA"},{"_id":59,"Tool_Name":"Benchling","ID":"59","Main_URL":"https://www.benchling.com/","Usage":"Data Storage","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Tool for DNA design (plasmids), & for keeping lab notes.\nBenchling is a cloud-based software platform for biology researchers and research and development organizations.\nIncludes: A Molecular Biology application to design novel engineered strains, a Registry application to build a library of custom entities and DNA parts, and an  inventory application to track the physical locations of samples. Benchling’s fully configurable Workflows application simplifies and standardizes the complex series of steps used in the assembly, testing, and generation of novel biological systems. Helps manage all omics-related results and provides the software foundation for developing engineered strains with superior performance characteristics. Provides Notebook, Workflow, and Registry applications that work in tandem to design, execute, document, and share process development studies on a single platform. Benchling’s Requests, Registry. Developer Platform integrate the analytical core with process development and manufacturing teams by providing a single platform to coordinate request generation, analytical results generation, and delivery of results. Workflows application, a developer platform for integrating with automation, and a unified software platform for centralizing upstream and downstream processes. \nTailored solutions for: Antibody related R&D, Cell Therapy, Gene Therapy, Proteins & Peptides, Vaccines, Industrial Biotech.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Freemiun","Pricing_Detail":"Free for academic use. Professional account starting at US$20.000/year with 5 users.","Documentation_and_Tutorials":"https://benchling.com/tutorials/5/simulating-digest","Alternative_URLs":"https://www.benchling.com/pricing/ https://www.crunchbase.com/organization/benchling https://www.linkedin.com/company/benchling/","Learning _Resources":"Sistemas Bioinformaticos","Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":60,"Tool_Name":"SnapGene","ID":"60","Main_URL":"https://www.snapgene.com/","Usage":"Data Storage","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Tool for DNA design (plasmids).\nSnapGene allows to plan, visualize, and document DNA cloning and PCR, annotate features and design primers.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Subscription only","Pricing_Detail":"> For Academic use: (users / USD yearly cost)\n1        $295\n2        $495\n5        $895\n10        $1,395\n\n> For Enterprise use: (users / USD yearly cost)\n1        $1,195\n2        $2,390\n5        $5,975\n10        $11,950","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.snapgene.com/buy-snapgene/","Learning _Resources":null,"Notes":null,"Year_Published":"2004","Country_or_Region":"USA"},{"_id":61,"Tool_Name":"Open MTA","ID":"61","Main_URL":"https://biobricks.org/openmta/","Usage":"Other","Biotech_Fields":"All","Description":"The OpenMTA (MTA: Material Transfer Agreement) is an easy-to-use legal tool that promotes exchange of biological materials. Was developed as a collaborative effort led by the BioBricks Foundation and the OpenPlant Synthetic Biology Research Centre with input from other stakeholders from across the globe. Research materials such as DNA, plasmids, microorganisms, proteins, seeds, and tissue samples are covered. The exchanges can take place between individual researchers or different organizations, including transfers of research materials between non-profit and for-profit sectors. Materials available under the OpenMTA are free of any royalty or fees, other than appropriate and nominal fees for preparation and distribution.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.openplant.org/openmta","Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":62,"Tool_Name":"Biocompare","ID":"62","Main_URL":"https://www.biocompare.com/","Usage":"Marketplace and Collaboration","Biotech_Fields":"All","Description":"Web platform that provides information and reviews for up-to-date product information, product reviews, and new technologies for life scientists. Provides specialized search tools, articles, product reviews, webinars, videos and technology spotlights all designed to ensure that Biocompare remains a trusted and comprehensive source of product information. \nBiocompare has built an online user experience to unite life science product buyers and sellers, providing targeted, integrated marketing channels: Product Listing, Flash-animated Advertising, E-mail Newsletter Sponsorship, New Technology Promotion, E-mail List Rental. All opportunities are available individually or as packages.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":"*Just for North America\n**Tool to search for more tools","Year_Published":"2000","Country_or_Region":"USA"},{"_id":63,"Tool_Name":"LabWorm","ID":"63","Main_URL":"https://labworm.com/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"Web repository to search digital tools for research. \nLabWorm is an aggregator of scientific online tools. \nLabWorm is also a Crowd Voting platform for the scientific community, allowing to vote on the various tools.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.linkedin.com/company/labworm/about/","Learning _Resources":null,"Notes":null,"Year_Published":"2015","Country_or_Region":"Israel"},{"_id":64,"Tool_Name":"Quartzy","ID":"64","Main_URL":"https://www.quartzy.com/","Usage":"Lab and Resource Management","Biotech_Fields":"All","Description":"Quartzy is a Lab management platform for inventoring and purchase. Quartzy provides the only complete solution for lab management that includes the world’s most comprehensive catalog of more than 3M lab supplies and deals backed by 1,000's of top suppliers. Trusted by 200,000 scientists across 13,000 labs nationwide, Quartzy streamlines inventory and purchasing communications to save labs time and money.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Freemiun","Pricing_Detail":"Free for non-profic use. Then starts at US$69 /month/3 users (+$29 /month/additional seats).","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/quartzy","Learning _Resources":null,"Notes":null,"Year_Published":"2009","Country_or_Region":"USA"},{"_id":65,"Tool_Name":"LabArchives","ID":"65","Main_URL":"https://www.labarchives.com/","Usage":"Lab and Resource Management","Biotech_Fields":"All","Description":"Electronic lab notebook (ELN). LabArchives provides a web-based software solution for storing, organizing, sharing and publishing scientific data. Much more than an Electronic Laboratory Notebook (ELN), LabArchives is a collaborative and publishing platform for research scientists.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Subscription only","Pricing_Detail":"Free with limited storage. Academic use for US$186/User/Year with 100GB/user. Enterprise use for US$372/User/Year with 100GB/user.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/labarchives","Learning _Resources":null,"Notes":null,"Year_Published":"2009","Country_or_Region":"USA"},{"_id":66,"Tool_Name":"QReserve","ID":"66","Main_URL":"https://get.qreserve.com/","Usage":"Lab and Resource Management","Biotech_Fields":"All","Description":"Lab Resource Management. QReserve helps laboratories and institutions manage, promote and share resources, expertise and facilities through their web platform, professional cataloguing services, and analytics tools. They provide unprecedented quantifiable data on utilization rates, associated revenues, capacity, and performance. Discover, access and purchase time on over ten thousand resources with institutions around the world.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Other pricing model","Pricing_Detail":"Base Academic Plan for Free. Unlimited Academic Plan for US$19/month. Premium Academic Plan for US$7/user/month.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/qreserve-inc","Learning _Resources":null,"Notes":null,"Year_Published":"2014","Country_or_Region":"Canada"},{"_id":67,"Tool_Name":"GraphPad","ID":"67","Main_URL":"https://www.graphpad.com/","Usage":"Data Analysis","Biotech_Fields":"All","Description":"GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers. (Alternatives to GraphPad Prism are SciDAVis, and interfaces to R).","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Subscription only","Pricing_Detail":"Student license for US$114 per year. Academic license starting at US$324/year with 2 users. Enterprise license starts at US$528/year with 2 users.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/graphpad-software","Learning _Resources":"Basic Statistics In Prism","Notes":null,"Year_Published":"1989","Country_or_Region":"USA"},{"_id":68,"Tool_Name":"Research Space","ID":"68","Main_URL":"https://www.researchspace.com/","Usage":"Lab and Resource Management","Biotech_Fields":"All","Description":"Electronic lab notebook (ELN)\nRSpace is a electronic lab notebook designed for deployment throughout academic research institutions, allowing to connect different laboratories in one space. The platform includes integrations for Protocols.io and other community platforms.\nAAS product.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Freemiun","Pricing_Detail":"Free for cloud service only and with unlimited storage. Enterprise options start at US$120/user/year.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/research-space","Learning _Resources":null,"Notes":null,"Year_Published":"2012","Country_or_Region":"USA"},{"_id":69,"Tool_Name":"Research Gate","ID":"69","Main_URL":"https://www.researchgate.net/","Usage":"Communication and Community","Biotech_Fields":"All","Description":"ResearchGate is an international social network for the scientific community. \nResearchGate is a European commercial social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a 2014 study by Nature and a 2016 article in Times Higher Education, it is the largest academic social network in terms of active users.\nFounded in 2008 by physicians Dr. Ijad Madisch and Dr. Sören Hofmayer, and computer scientist Horst Fickenscher, ResearchGate has more than 17 million members today.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2008","Country_or_Region":"USA"},{"_id":70,"Tool_Name":"Science Exchange","ID":"70","Main_URL":"https://www.scienceexchange.com/","Usage":"Lab and Resource Management","Biotech_Fields":"All","Description":"R&D Services Management company. The Science Exchange Marketplace automates collaborative tasks between scientific service buyers and providers, such as obtaining quotes, managing projects and processing payments, all with rigorous data security and regulatory compliance embedded throughout.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Usage based","Pricing_Detail":"A fee of approximately 5% is charged to the customer.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/science-exchange","Learning _Resources":null,"Notes":null,"Year_Published":"2011","Country_or_Region":"USA"},{"_id":71,"Tool_Name":"Rheaply","ID":"71","Main_URL":"https://www.rheaply.com/","Usage":"Marketplace and Collaboration","Biotech_Fields":"All","Description":"Asset Exchange Manager. Rheaply provides an on-line asset management platform which enables better resource visibility and utilization. Rheaply enables to create a marketplace to buy, sell, trade, donate, and rent resources within an organization or externally.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Other pricing model","Pricing_Detail":null,"Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2016","Country_or_Region":"USA"},{"_id":72,"Tool_Name":"Biorender","ID":"72","Main_URL":"https://biorender.com/","Usage":"Visualization","Biotech_Fields":"All","Description":"Biorender is a web-based software tool that enables scientists and to create and share high-quality science figures in a simple manner. BioRender has developed a database of thousands of scientific icons and templates with “drag-and-drop” functionality to create scientific illustrations.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Freemiun","Pricing_Detail":"Free for educational use. Single user account for US$35/month, 5 users for US$99/month.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/biorender-inc","Learning _Resources":null,"Notes":null,"Year_Published":"2017","Country_or_Region":"USA"},{"_id":73,"Tool_Name":"BioJava","ID":"73","Main_URL":"https://biojava.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Open-source java library for bioinformatics. BioJava is an open-source project dedicated to providing a Java library for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of biological sequences and 3D structures. The main goal of the project is to facilitate rapid application development for bioinformatics.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2000","Country_or_Region":"UK"},{"_id":74,"Tool_Name":"Galaxy","ID":"74","Main_URL":"https://usegalaxy.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.\nIs a platform that has centralized several tools, but with some limitations, like not offering the flexibility of a console/terminal.\nGalaxy is an open, web-based platform for data intensive biomedical research. The Galaxy team is a part of BX at Penn State, and the Biology department at Johns Hopkins University. The Galaxy Project is supported in part by NHGRI, NSF, The Huck Institutes of the Life Sciences, The Institute for CyberScience at Penn State, and Johns Hopkins.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"http://www.bioinformatics.nl/galaxy https://en.wikipedia.org/wiki/Galaxy_(computational_biology)","Learning _Resources":"Sistemas Bioinformaticos,Next Generation Sequencing Platforms and Bioinformatics Analysis,Galaxy introduction for life scientists,Systems Biology and Biotechnology Specialization,Genomic Data Science with Galaxy,Whole Genome Variant Calling @ Galaxy","Notes":null,"Year_Published":"2005","Country_or_Region":"USA"},{"_id":75,"Tool_Name":"Data Biosphere","ID":"75","Main_URL":"https://www.databiosphere.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Interoperable platforms for next generation of biomedical research, looks to build an open, compatible, and secure approach to data within the larger research community.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2017","Country_or_Region":"USA"},{"_id":76,"Tool_Name":"Terra","ID":"76","Main_URL":"https://terra.bio/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Terra is an open data ecosystem that is accessible and equitable to the worldwide research community. Is a scalable infrastructure to connect data repositories on the cloud and allow researchers to perform integrative analyses reproducibly across datasets at massive scale.\nAccess data, run analysis tools, and collaborate within the biomedical research community. \nUp to October 2021 Terra claimed to have 19,942 users in its platform.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Freemiun","Pricing_Detail":null,"Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":77,"Tool_Name":"Gen3","ID":"77","Main_URL":"https://gen3.org/","Usage":"Data Storage","Biotech_Fields":"Bioinformatics/Computational Biology,Biostatistics,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics","Description":"Gen3 is an open source and cloud-based platform for developing for managing, analyzing, harmonizing, and sharing large datasets.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":78,"Tool_Name":"Dockstore","ID":"78","Main_URL":"https://dockstore.org/","Usage":"Data Storage","Biotech_Fields":"All","Description":"Dockstore is an open platform used by the GA4GH for sharing Docker-based tools described with either the Common Workflow Language (CWL), the Workflow Description Language (WDL), or Nextflow. Developed by the Cancer Genome Collaboratory.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":79,"Tool_Name":"Global Alliance for Genomics and Health (GA4GH)","ID":"79","Main_URL":"https://www.ga4gh.org/","Usage":"Other","Biotech_Fields":"Physiology,Neurobiology,Immunology,Pharmacology,Epidemiology,Oncology,Biomedicine","Description":"The Global Alliance for Genomics and Health (GA4GH) is an international, nonprofit alliance formed in 2013 to accelerate the potential of research and medicine to advance human health. Bringing together 600+ leading organizations working in healthcare, research, patient advocacy, life science, and information technology, the GA4GH community is working together to create frameworks and standards to enable the responsible, voluntary, and secure sharing of genomic and health-related data.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2013","Country_or_Region":"International"},{"_id":80,"Tool_Name":"Riffyn","ID":"80","Main_URL":"https://riffyn.com/","Usage":"Data Analysis","Biotech_Fields":"All","Description":"Data processing platform. \nRiffyn is a platform for addressing scientific workflows and data. Cloud-based software that provides computer-aided process design and advanced data analytics to R&D organizations. Riffyn delivers data quality and real-time collaboration capabilities for reproducible discoveries and product development.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Other pricing model","Pricing_Detail":null,"Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.crunchbase.com/organization/riffyn","Learning _Resources":null,"Notes":null,"Year_Published":"2014","Country_or_Region":"USA"},{"_id":81,"Tool_Name":"Benchsci","ID":"81","Main_URL":"https://www.benchsci.com/","Usage":"Data Analysis","Biotech_Fields":"Physiology,Neurobiology,Immunology,Pharmacology,Oncology,Biomedicine","Description":"Benchsci uses advanced biomedical artificial intelligence (AI) to  increase the speed and quality of health research. \nAI-Assisted Experiment Design platform. Their technology guides experimental design and preclinical R&D serving over 40,000 scientists, working at more than 4,300 institutions worldwide. Benefits: quantifiable productivity gains, reduction in spend, and recouped scientist capacity.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Freemiun","Pricing_Detail":"Free for academic use.","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2015","Country_or_Region":"Canada"},{"_id":82,"Tool_Name":"GIGADB","ID":"82","Main_URL":"http://gigadb.org/","Usage":"Repository and DB","Biotech_Fields":"All","Description":"GigaDB (GigaScience DataBase) is a disciplinary repository launched in 2011 with the aim of ensuring long-term access to massive multidimensional datasets from life science and biomedical science studies. The datasets are diverse and include genomic, transcriptomic, and imaging data. The datasets are curated by GigaDB biocurators who are employed by BGI and China National GeneBank.\nGigaDB contains 1958 discoverable, trackable, and citable datasets that have been assigned DOIs and are available for public download and use.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2011","Country_or_Region":"China"},{"_id":83,"Tool_Name":"Pymol","ID":"83","Main_URL":"https://pymol.org/2/","Usage":"Visualization","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology,Biophysics","Description":"Molecular visualization tool. \nPyMOL is an open source molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Freemiun","Pricing_Detail":"Free for educational purposes. The Professional License for one person is US$99/year. Laboratory & Classroom License for one researcher/instructor and his/her students for US$269.","Documentation_and_Tutorials":null,"Alternative_URLs":"https://pymol.org/2/buy.html?q=buy","Learning _Resources":null,"Notes":null,"Year_Published":"2000","Country_or_Region":"USA"},{"_id":84,"Tool_Name":"Rasmol","ID":"84","Main_URL":"http://www.openrasmol.org/","Usage":"Visualization","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology,Biophysics","Description":"Molecular visualization tool. \nRasMol is a program for molecular graphics visualisation, used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.sciencedirect.com/science/article/abs/pii/S0968000400890805","Learning _Resources":"Foundations of Computational and Systems Biology","Notes":null,"Year_Published":"1992","Country_or_Region":"UK"},{"_id":85,"Tool_Name":"Swiss-PdbViewer","ID":"85","Main_URL":"https://spdbv.vital-it.ch/","Usage":"Visualization","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology,Biophysics","Description":"Molecular visualization tool. \nSwiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) in collaboration between GlaxoSmithKline R&D and the Structural Bioinformatics Group at the Biozentrum in Basel","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":"Foundations of Computational and Systems Biology,Computation for Biological Engineers","Notes":null,"Year_Published":null,"Country_or_Region":"Switzerland"},{"_id":86,"Tool_Name":"Swiss-Model","ID":"86","Main_URL":"http://swissmodel.expasy.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology,Biophysics","Description":"Swiss-Model is an automated comparative protein modelling server. \nFully automated protein structure homology-modelling server, accessible via the Expasy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make protein modelling accessible to all life science researchers worldwide.\nIt requires a viewer such as DeepView - Swiss-PdbViewer, Rasmol , Cn3Dv3.0 or WebMolJavaPDB.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"Switzerland"},{"_id":87,"Tool_Name":"3DNA","ID":"87","Main_URL":"https://x3dna.org/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology,Biophysics","Description":"3DNA is an integrated software system for the analysis, rebuilding, and visualization of 3D nucleic-acid-containing structures. The software is applicable not only to DNA but also to complicated RNA structures and DNA-protein complexes.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":"https://pubmed.ncbi.nlm.nih.gov/12930962/","Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"USA"},{"_id":88,"Tool_Name":"QUAST – Quality Assessment Tool for Genome Assemblies","ID":"88","Main_URL":"http://quast.sourceforge.net/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. This document provides instructions for the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, QUAST-LG, the extension for large genomes (e.g., mammalians), and Icarus, the interactive visualizer for these tools.\n\nYou can find key project news and the latest version of the tool at http://quast.sf.net/. We also post all our news and related stuff on Twitter.\n\nQUAST default pipeline utilizes Minimap2. Functional elements prediction modules use GeneMarkS, GeneMark-ES, GlimmerHMM, Barrnap, and BUSCO. QUAST module for finding structural variations applies BWA, Sambamba, and GRIDSS. Also we use bedtools for calculating raw and physical read coverage, which is shown in Icarus contig alignment viewer. Icarus also can use Circos if it is installed in PATH. QUAST-LG introduced modules requiring KMC and Red. In addition, MetaQUAST uses MetaGeneMark, Krona tools, BLAST, and SILVA 16S rRNA database.\nAlmost all tools listed above are built in into the QUAST package which is ready for use by academic, non-profit institutions and U.S. Government agencies. If you are not in one of these categories please refer to LICENSE section 'Third-party tools incorporated into QUAST' for guidelines on how to complete the licensing process.\n\nVersion 5.0.2 of QUAST was released under GPL v2 on November 22, 2018. Note that some of build-in third-party tools are not under GPL v2. See LICENSE for details.\n\nMetaQUAST (Mikheenko et al., 2016) is a tool specifically designed for the quality assessment of metagenomics assemblies. Amongst other things, MetaQUAST uses alignment of the original reads to the assembled data to enable detection of putative structural variants and mis-assemblies.","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":"http://quast.sourceforge.net/docs/manual.html","Alternative_URLs":"https://github.com/ablab/quast","Learning _Resources":"Long-read Bioinformatics,Introduction to Metagenomic Data Analysis","Notes":null,"Year_Published":"2015","Country_or_Region":null},{"_id":89,"Tool_Name":"MetaVelvet","ID":"89","Main_URL":"http://metavelvet.dna.bio.keio.ac.jp/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"MetaVelvet (Namiki et al., 2012) is a metagenomic de novo assembler, extending the single-genome assembler Velvet.\nAn important step in metagenomics analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines use a single-genome assembler with carefully optimized parameters. A limitation of a single-genome assembler for de novo metagenome assembly is that sequences of highly abundant species are likely misidentified as repeats in a single genome, resulting in a number of small fragmented scaffolds. We extended a single-genome assembler for short reads, known as Velvet, to metagenomic assembly for mixed short reads of multiple species","Technology_Type":"Desktop/Mobile App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2012","Country_or_Region":null},{"_id":90,"Tool_Name":"GeneOrder","ID":"90","Main_URL":"http://www.geneorder.org/server.php","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"GeneOrder 2.0 It is an ideal tool for the alignment of\nsmall GenBank genome sequences (upto 0.25Mb). It has a new version as GeneOrder 3.0. There are two display formats: graphical and tabular.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":null},{"_id":91,"Tool_Name":"CoreGenes","ID":"91","Main_URL":"http://binf.gmu.edu:8080/CoreGenes4.0/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"CoreGenes is designed to analyze two to five genomes simultaneously, it also generates a table of related genes i.e. orthologs and putative orthologs. It has a limit of 0.35 Mb. It has an updatedversion Core Genes 2.0.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":null},{"_id":92,"Tool_Name":"BASys","ID":"92","Main_URL":"http://basys.ca/basys/cgi/submit.pl","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"BASys It is known as Bacterial Annotation Tool. It is far-fetched tool which supports automated and in-depth annotation of bacterial genomic sequences .","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":null,"Documentation_and_Tutorials":null,"Alternative_URLs":"https://www.hsls.pitt.edu/obrc/index.php?page=URL1132678306","Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":"Canada"},{"_id":93,"Tool_Name":"RNAsoft","ID":"93","Main_URL":"http://www.rnasoft.ca/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"Software for RNA/DNA secondary structure prediction and design. RNAsoft: RNAsoft is a collection of online services for the computational prediction and design of RNA/DNA structure. Three programs are currently available in RNAsoft are Pair fold, comb fold and RNA designer. (http://www.rnasoft.ca/)","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":null},{"_id":94,"Tool_Name":"DNA Shape","ID":"94","Main_URL":"https://rohslab.usc.edu/DNAshape/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res., 41, W56-W62.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":"2013","Country_or_Region":"USA"},{"_id":95,"Tool_Name":"Motif","ID":"95","Main_URL":"https://www.genome.jp/tools/motif/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"Tool for genetic sequence motif search.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Basic to Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":null},{"_id":96,"Tool_Name":"Tree","ID":"96","Main_URL":"https://www.genome.jp/tools-bin/ete","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology","Description":"Phylogenetic analysis pipeline by ETE3.","Technology_Type":"Web based/Cloud App","Level_of_Complexity":"Advanced","Pricing_Model":"Free / Open Source","Pricing_Detail":"--","Documentation_and_Tutorials":null,"Alternative_URLs":null,"Learning _Resources":null,"Notes":null,"Year_Published":null,"Country_or_Region":null},{"_id":97,"Tool_Name":"The Viral Proteomic Tree server","ID":"97","Main_URL":"https://www.genome.jp/viptree/","Usage":"Data Analysis","Biotech_Fields":"Bioinformatics/Computational Biology,Genetic Engineering,Transcriptomics,Proteomics,Metabolomics,Molecular Biology,Microbiology,Immunology","Description":"The ViPTree server generates a \"proteomic tree\" of viral genome sequences based on genome-wide sequence similarities computed by tBLASTx. The original proteomic tree concept (i.e., \"the Phage Proteomic Tree”) was developed by Rohwer and Edwards, 2002. A proteomic tree is a dendrogram that reveals global genomic similarity relationships between tens, hundreds, and thousands of viruses. It has been shown that viral groups identified in a proteomic tree well correspond to established viral taxonomies. 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