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A a configurable software package for peptide and protein mass spectrometry analyses. It includes the SEQUEST search algorithm to identify separate proteins in complex mixtures, interactive navigation tools to filter and sort protein summaries, customized spectral plots, and chromatograms using the PEPMATCH and PEPMAP tools. This software also has batch processing capabilities to improve throughput by queuing up several files, and custom-build proprietary databases, index databases, and retrieve databases through a public server.
Proper citation: BioWorks (RRID:SCR_014594) Copy
http://compbio.mit.edu/cummeRbund/index.html
Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.
Proper citation: CummeRbund (RRID:SCR_014568) Copy
http://csbg.cnb.csic.es/mbrole/
Software program for overrepresentation (enrichment) analysis of categorical annotations for a set of compounds. These categorical annotations correspond to biological and chemical information found in public databases and software. Annotations can be biological (pathways, enzyme interactions, pharmacological action) or chemical (taxonomy and chemical groups).
Proper citation: MBRole (RRID:SCR_014684) Copy
https://www.schrodinger.com/Phase/
Pharmacophore modeling software to create 3D structure activity relationships, screen databases, and generate hits through establishing a chemical space occupied by active ligands. Used in drug design.
Proper citation: Phase (RRID:SCR_014884) Copy
Database for visualizing and making use of public ChIP-seq data. ChIP-Atlas covers almost all public ChIP-seq experiments and data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA.
Proper citation: ChIP-Atlas (RRID:SCR_015511) Copy
Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action.
Proper citation: DrugCentral (RRID:SCR_015663) Copy
Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions.
Proper citation: MacVector (RRID:SCR_015700) Copy
http://www.diagram-consortium.org/
Consortium of researchers aiming to characterize the genetic basis of type 2 diabetes with a principal focus on samples of European descent. DIAGRAM also features a database of DIAGRAM publications and diabetes-related research data.
Proper citation: DIAGRAM (RRID:SCR_015675) Copy
Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences.
Proper citation: X!Tandem (RRID:SCR_015645) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 6,2026. Platform for mediation and integration of schizophrenia neuroimaging-related databases. It provides access to federated databases, novel mediation software, and large-scale data-sharing features.
Proper citation: SchizConnect (RRID:SCR_015766) Copy
http://ualcan.path.uab.edu/cgi-bin/ualcan-res.pl
Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses.
Proper citation: UALCAN (RRID:SCR_015827) Copy
http://app.cgu.edu.tw/circlnc/
Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data.
Proper citation: circlncRNAnet (RRID:SCR_015794) Copy
A non-governmental, non-profit public database for paleontological data providing researchers and the public with information about the entire fossil record. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database's broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions. Paleontological data files are accepted for upload. However, PaleoBioDB needs some basic data types to be included in order to perform an upload. The Application Programming Interface (API) gives scientists, students, and developers programmatic access to taxonomic, spatial, and temporal data contained within the database.
Proper citation: Paleobiology Database (RRID:SCR_003798) Copy
http://www.innomed-addneuromed.com/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee.
Proper citation: AddNeuroMed (RRID:SCR_003819) Copy
Project to develop a drug safety database from the pharmaceutical industry legacy toxicology reports and public toxicology data; innovative in silico strategies and novel software tools to better predict the toxicological profiles of small molecules in early stages of the drug development pipeline. The project is creating this pharmaco-toxicological database with an aim to: * Reduce the number of animal tests * Decrease the attrition rates of new drug candidates * Increase the success rate of new molecular entities becoming drugs * Improve the safety of drugs on the market The project consists of three different systems, * eTOX VITIC Database a unified database containing all confidential and non-confidential data collected in eTOX (historical data from the pharmaceutical industry) * ChOX Database a unified database containing public data (literature and public database) * eTOXsys Query and Prediction System an interface providing a uniform access to the two databases (VITIC and ChOX) and to all developed prediction models and systems
Proper citation: eTOX (RRID:SCR_003712) Copy
GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University as part of the research projects. GenomeNet is operated using the Supercomputer System of the Institute for Chemical Research, Kyoto University. LinkDB is supported by the National Bioscience Database Center of the Japan Science and Technology Agency.
Proper citation: GenomeNet (RRID:SCR_004165) Copy
A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version.
Proper citation: bioRxiv (RRID:SCR_003933) Copy
The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).
Proper citation: NIMH Data Archive (RRID:SCR_004434) Copy
http://discovery.hsci.harvard.edu/
An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket.
Proper citation: Stem Cell Discovery Engine (RRID:SCR_004453) Copy
Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.
Proper citation: FigShare (RRID:SCR_004328) Copy
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