Tools   Select Another Resource Report Type

http://tgrc.ucdavis.edu/

Genebank of wild relatives, monogenic mutants and miscellaneous genetic stocks of tomato. TGRC offers seed samples for free to researchers worldwide.

Proper citation: C.M. Rick Tomato Genetic Resources Center (RRID:SCR_014954) Copy   

•   Source: SciCrunch Registry

http://www.vtk.org

Cross-platform visualization software system for 3D computer graphics, image processing, and data visualization. Various visualization algorithms and advanced modeling techniques are supported within VTK, as well as parallel processing and interoperability with select databases.

Proper citation: VTK (RRID:SCR_015013) Copy   

•   Source: SciCrunch Registry

http://www.brainbank.nl

A biomaterial supply resource which collects, stores, and disseminates diseased and healthy brain tissue. The Netherlands Brain Bank currently contains more than 3600 samples, and each sample includes a neuropathological report and donor medical history. The samples can additionally be matched with ante-mortem parameters and post-mortem parameters upon request. Sample types include cortex, spinal cord, cerebrospinal fluid, plasma, and DNA, among others. Database mining is available with a financial contribution.

Proper citation: Netherlands Brain Bank (RRID:SCR_013841) Copy   

•   Source: SciCrunch Registry

http://www.optibrium.com/stardrop/index.php

Software toolkit for drug design and discovery, including plugins for in silico compound optimization, compound selection and integration into other databases.

Proper citation: StarDrop (RRID:SCR_014902) Copy   

•   Source: SciCrunch Registry

http://www.rdkit.org/

An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website.

Proper citation: RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) Copy   

•   Source: SciCrunch Registry

http://prospector.ucsf.edu

A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass.

Proper citation: Protein Prospector (RRID:SCR_014558) Copy   

•   Source: SciCrunch Registry

https://www.molinspiration.com/

Broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Molinspiration tools are platform independent and may be run on any PC, Mac, UNIX or LINUX machine. Software is distributed in form of engines, which may be used as stand-alone computational engines, used to power web-based tools, or incorporated into larger in-house Java applications.

Proper citation: Molinspiration (RRID:SCR_018525) Copy   

•   Source: SciCrunch Registry

https://www.ngvbcc.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology.

Proper citation: National Gene Vector Biorepository (RRID:SCR_004760) Copy   

•   Source: SciCrunch Registry

http://www.simcyp.com/

Research based company providing predictive pharmacokinetic and pharmacodynamic tools, workshops and consultancy services. Their user-friendly simulator and databases predict drug absorption, clearance, distribution and metabolic drug-drug interactions from in vitro data. Simcyp's clients include major global pharmaceutical and bioscience companies, leading academic institutes and regulatory authorities. These clients form the Simcyp Consortium, which together with independent International Scientific Advisory Board, guide scientific development at Simcyp.Simcyp was acquired by Certara in 2012.

Proper citation: Simcyp (RRID:SCR_003944) Copy   

•   Source: SciCrunch Registry

http://sequenceontology.org/

A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.

Proper citation: SO (RRID:SCR_004374) Copy   

•   Source: SciCrunch Registry

http://www.human-phenotype-ontology.org/

Provides standardized vocabulary of phenotypic abnormalities encountered in human disease. Structured and controlled vocabulary for phenotypic features encountered in human hereditary and other disease. HPO is being developed in collaboration with members of OBO Foundry (Open Biological and Biomedical Ontologies), and logical definitions for HPO terms are being developed using PATO and a number of other ontologies including FMA, GO, ChEBI, and MPATH.

Proper citation: Human Phenotype Ontology (RRID:SCR_006016) Copy   

•   Source: SciCrunch Registry

http://www.cochrane.org/editorial-and-publishing-policy-resource/cochrane-central-register-controlled-trials-central

A bibliographic database that provides a highly concentrated source of reports of randomized controlled trials. Records contain the list of authors, the title of the article, the source, volume, issue, page numbers, and, in many cases, a summary of the article (abstract). They do not contain the full text of the article. Cochrane Groups maintain and update Specialized Registers, which are collections of controlled trials relevant to the groups. CENTRAL is comprised of these Specialized Registers, relevant records retrieved from MEDLINE and EMBASE, and records retrieved through handsearching (planned manual searching of a journal or conference proceedings to identify all reports of randomized controlled trials and controlled clinical trials). The Cochrane Collaboration contracts a technology company, Metaxis, to merge the records from the sources outlined above and provide a data feed to the publisher. New and changed data are delivered to the publisher on a monthly basis.

Proper citation: Cochrane Central Register of Controlled Trials (RRID:SCR_006576) Copy   

•   Source: SciCrunch Registry

http://www.numpy.org

NumPy is the fundamental package needed for scientific computing with Python. It contains among other things: * a powerful N-dimensional array object * sophisticated (broadcasting) functions * tools for integrating C/C and Fortran code * useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Sponsored by ENTHOUGHT

Proper citation: NumPy (RRID:SCR_008633) Copy   

•   Source: SciCrunch Registry

http://www.seqtools.dk/

A large collection of tools for basic and advanced analyses of nucleotide and protein sequences. The tools are wrapped into a common user interface making handling, storage, retrieval and viewing the results easy and logical. A seqtools project can accommodate many thousand sequences making unattended batch analyses like database searching at NCBI painless with the robust search engine included in seqtools.

Proper citation: SEQtools (RRID:SCR_008579) Copy   

•   Source: SciCrunch Registry

https://bioinf.eva.mpg.de/patman/

Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PatMaN (RRID:SCR_011821) Copy   

•   Source: SciCrunch Registry

http://infernal.janelia.org/

Software for searching DNA sequence databases for RNA structure and sequence similarities.

Proper citation: Infernal (RRID:SCR_011809) Copy   

•   Source: SciCrunch Registry

http://www.hmdb.ca

Curated collection of human metabolite and human metabolism data which contains records for endogenous metabolites, with each metabolite entry containing detailed chemical, physical, biochemical, concentration, and disease information. This is further supplemented with thousands of NMR and MS spectra collected on purified reference metabolites.

Proper citation: HMDB (RRID:SCR_007712) Copy   

•   Source: SciCrunch Registry

http://mmcd.nmrfam.wisc.edu/

A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.

Proper citation: Madison Metabolomics Consortium Database (RRID:SCR_007803) Copy   

•   Source: SciCrunch Registry

http://rebase.neb.com/rebase/

Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.,

Proper citation: REBASE (RRID:SCR_007886) Copy   

•   Source: SciCrunch Registry

http://www.obofoundry.org/

A collaboration involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, this site provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. Feedback is welcome and participation encouraged.

Proper citation: OBO (RRID:SCR_007083) Copy   

•   Source: SciCrunch Registry