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http://treestoolbox.org/

Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.

Proper citation: TREES toolbox (RRID:SCR_010457) Copy   

•   Source: SciCrunch Registry

http://www.evocontology.org/site/Main/EvocOntologyDotOrg

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.

Proper citation: eVOC (RRID:SCR_010704) 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

http://gene3d.biochem.ucl.ac.uk/Gene3D/

A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gene3D (RRID:SCR_007672) Copy   

•   Source: SciCrunch Registry

http://genomics.senescence.info/

Collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available.

Proper citation: Human Ageing Genomic Resources (RRID:SCR_007700) Copy   

•   Source: SciCrunch Registry

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.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy   

•   Source: SciCrunch Registry

http://www.guidetopharmacology.org

Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target.

Proper citation: IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) Copy   

•   Source: SciCrunch Registry

http://genomics.senescence.info/diet/

Database of genes associated with dietary restriction. It includes genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of dietary restriction and genes robustly altered due to dietary restriction, derived from a meta-analysis of microarray studies in mammals.

Proper citation: Dietary Restriction Gene Database (RRID:SCR_013720) Copy   

•   Source: SciCrunch Registry

https://github.com/alexlib/KymoButler-1

Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis.

Proper citation: KymoButler (RRID:SCR_021717) Copy   

•   Source: SciCrunch Registry

https://shiny.cnsgenomics.com/mRnd/

Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach.

Proper citation: mRnd (RRID:SCR_022156) Copy   

•   Source: SciCrunch Registry

http://www.biomart.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.

Proper citation: BioMart Project (RRID:SCR_002987) Copy   

•   Source: SciCrunch Registry

https://opentrials.net/

Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally.

Proper citation: Open Trials (RRID:SCR_015570) Copy   

•   Source: SciCrunch Registry

http://mousebrain.org/

Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.

Proper citation: mousebrain.org (RRID:SCR_016999) Copy   

•   Source: SciCrunch Registry

http://geroprotectors.org

Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases.

Proper citation: GEROprotectors (RRID:SCR_016737) Copy   

•   Source: SciCrunch Registry

https://github.com/kjolley/BIGSdb

Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level.

Proper citation: BIGSdb (RRID:SCR_023551) 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

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