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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
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
http://tree.bio.ed.ac.uk/software/seqgen/
Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.
Proper citation: Seq-Gen (RRID:SCR_014934) Copy
Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes.
Proper citation: DECIPHER (RRID:SCR_006552) Copy
An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.
Proper citation: MEROPS (RRID:SCR_007777) Copy
http://supfam.mbu.iisc.ernet.in/index.html
SUPFAM is a database that consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 3.0) of SUPFAM uses homologous families in Pfam (Version 23.0) and SCOP (Release 1.69) which are examples of sequence -alignment and structure classification databases respectively. The two steps involved in setting up of SUPFAM database are * Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information. * An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies. The SUPFAM database can be used in either the Browse mode or Search mode. In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed. In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SUPFAM (RRID:SCR_005304) Copy
https://sites.google.com/site/depressiondatabase/
The Major Depressive Disorder Neuroimaging Database (MaND) contains information of 225 studies which have investigated brain structure (using MRI and CT scans) in patients with major depressive disorder compared to a control group. 143 studies and 63 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website.
Proper citation: Major depressive disorder neuroimaging database (RRID:SCR_005835) Copy
Ratings or validation data are available for this resource
Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
Proper citation: GENCODE (RRID:SCR_014966) Copy
https://github.com/JCVenterInstitute/NSForest/releases
Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy.
Proper citation: NS-Forest (RRID:SCR_018348) Copy
Collection of human embryonic and fetal material (Tissue and RNA) ranging from 3 to 20 weeks of development available to the international scientific community. Material can either be sent to registered users or our In House Gene Expression Service (IHGES) can carry out projects on user''''s behalf, providing high quality images and interpretation of gene expression patterns. Gene expression data emerging from HDBR material is added to our gene expression database which is accessible via our HUDSEN (Human Developmental Studies Network) website. A significant proportion of the material has been cytogenetically karyotyped, and normal karyotyped material is provided for research.
Proper citation: Human Developmental Biology Resource (RRID:SCR_006326) Copy
Web application as repository and launch platform for Psychopy experiments and other open-source tools.
Proper citation: Pavlovia (RRID:SCR_023320) Copy
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
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
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
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
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
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
https://github.com/xavierdidelot/clonalorigin
Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.
Proper citation: ClonalOrigin (RRID:SCR_016061) Copy
https://sanger-pathogens.github.io/Roary/
Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.
Proper citation: Roary (RRID:SCR_018172) Copy
https://github.com/linnarsson-lab/cytograph
Software multistage analysis pipeline which progressively discovers cell types or states while mitigating impact of technical artifacts.Used for single cell analysis.
Proper citation: Cytograph (RRID:SCR_023101) Copy
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