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http://www.cellml.org/models

Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.

Proper citation: CellML Model Repository (RRID:SCR_008113) Copy   

•   Source: SciCrunch Registry

http://www.cellml.org/

The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.

Proper citation: CellML (RRID:SCR_008061) Copy   

•   Source: SciCrunch Registry

http://www.orcid.org/

Non-profit organization dedicated to solving the author/contributor name ambiguity problem in scholarly communications by creating a central registry of unique identifiers for individual researchers and an open and transparent linking mechanism between ORCID and other current author ID schemes. These identifiers, and the relationships among them, can be linked to the researcher''s output to enhance the scientific discovery process and to improve the efficiency of research funding and collaboration within the research community. The ideal solution is to establish a registry that is adopted and embraced as the de facto standard by the whole of the community. A resolution to the systemic name ambiguity problem, by means of assigning unique identifiers linkable to an individual''s research output, will enhance the scientific discovery process and improve the efficiency of funding and collaboration. The organization brings together the leaders of the most influential universities, funding organizations, societies, publishers and corporations from around the globe and is managed by a fourteen member Board of Directors. A disambiguated set of authors will allow new services and benefits to be built for the research community by all stakeholders in scholarly communication: from commercial actors to non-profit organizations, from governments to universities.

Proper citation: ORCID - Open Researcher and Contributor ID (RRID:SCR_008700) Copy   

•   Source: SciCrunch Registry

http://www.biomart.org/biomart/martview/ddb9ce1ad275cde372c968d13fa11f5f

A web server interface of BioMart software and provides a unified view over disparate data sources that enable bioscientists to retrieve data from one or multiple sources in a simple and efficient way. This MartView web server features seamless data federation making cross querying of data sources in a user friendly and unified way. Data sources include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase, etc. The web server not only provides access through a web interface, it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services.

Proper citation: BioMart MartView (RRID:SCR_010714) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/ariba

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

Proper citation: Ariba (RRID:SCR_015976) Copy   

•   Source: SciCrunch Registry

http://www.functionalnet.org/humannet/about.html

Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.

Proper citation: HumanNet (RRID:SCR_016146) Copy   

•   Source: SciCrunch Registry

https://github.com/HicServices/RDMP/wiki

Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.

Proper citation: Research Data Management Platform (RRID:SCR_016268) Copy   

•   Source: SciCrunch Registry

https://github.com/robince/gcmi

Software package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula.

Proper citation: Gaussian-Copula Mutual Information (GCMI) (RRID:SCR_016450) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools.

Proper citation: PALM (RRID:SCR_017029) Copy   

•   Source: SciCrunch Registry

http://www.vasotracker.com

Open source and stand alone software for assessing vascular reactivity. Used in pressure myograph system.

Proper citation: VasoTracker (RRID:SCR_017233) Copy   

•   Source: SciCrunch Registry

http://www.ariesepigenomics.org.uk/

Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.

Proper citation: Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) Copy   

•   Source: SciCrunch Registry

https://models.physiomeproject.org

Repository of mainly CellML models powered by collection of software tools and libraries with PMR2 software suite as core power. Third party integration suites are RICORDO, Virtuoso, BiVeS/BudHat, OpenCOR, CombineArchive Web, WebCAT, Morre/MaSyMoS.

Proper citation: Physiome Model Repository (RRID:SCR_017374) Copy   

•   Source: SciCrunch Registry

http://europepmc.org/

Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts.

Proper citation: Europe PubMed Central (RRID:SCR_005901) Copy   

•   Source: SciCrunch Registry

https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT

Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.

Proper citation: NeuroChaT (RRID:SCR_018020) Copy   

•   Source: SciCrunch Registry

https://www.rappsilberlab.org/software/xisearch/

Software and algorithm for analyzing protein protein cross linking mass spectrometry data. Library of routines for peptide based mass spectrometry. Contains search engine for identification of crosslinked peptides.

Proper citation: xiSEARCH (RRID:SCR_018395) Copy   

•   Source: SciCrunch Registry

http://web.cbio.uct.ac.za/~darren/rdp.html

Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.

Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@Tracer@v1.6

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

https://www.openmicroscopy.org/site/products/bio-formats

Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard.

Proper citation: Bio-Formats (RRID:SCR_000450) Copy   

•   Source: SciCrunch Registry

http://zebrafishucl.org/zebrafishbrain#about-1

Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

Proper citation: Zebrafish Brain Atlas (RRID:SCR_000606) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry