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https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.
Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy
https://swissmodel.expasy.org/
Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists.
Proper citation: SWISS-MODEL (RRID:SCR_018123) Copy
Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.
Proper citation: SIGNOR (RRID:SCR_018485) Copy
https://edspace.american.edu/openbehavior/project/facesync/, https://bio.tools/FaceSync
Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.
Proper citation: FaceSync project (RRID:SCR_021393) Copy
A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.
Proper citation: EvidenceFinder (RRID:SCR_013764) Copy
https://github.com/princelab/mspire-simulator
A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components.
Proper citation: Mspire-Simulator (RRID:SCR_001431) Copy
http://img.jgi.doe.gov/cgi-bin/m/main.cgi
Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets.
Proper citation: IMG System (RRID:SCR_002965) Copy
A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.
Proper citation: EchoBASE (RRID:SCR_002430) Copy
http://www.tanpaku.org/autophagy/
Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes.
Proper citation: Autophagy Database (RRID:SCR_002671) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014)
Proper citation: DOMINE: Database of Protein Interactions (RRID:SCR_002399) Copy
Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: VIPERdb (RRID:SCR_002853) Copy
An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.
Proper citation: Human Gene Connectome Server (RRID:SCR_002627) Copy
A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF).
Proper citation: Nucleic Acid Database (RRID:SCR_003255) Copy
http://www.ncbi.nlm.nih.gov/RefSeq/
Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
Proper citation: RefSeq (RRID:SCR_003496) Copy
Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene.
Proper citation: MutDB (RRID:SCR_003251) Copy
http://webdocs.cs.ualberta.ca/~bioinfo/PA/Sub/
Web server specialized to predict the subcellular localization of proteins using established machine learning techniques.
Proper citation: Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) Copy
http://compbio.uthsc.edu/miRSNP/
Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.
Proper citation: PolymiRTS (RRID:SCR_003389) Copy
http://nar.oxfordjournals.org/content/34/suppl_2/W635.long
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 9, 2016. A web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by deploying more Web wrapper agents. FASTSNP provides three options for users to submit requests. If users already have some candidate SNPs on a candidate gene, they may use Query by Candidate Gene to select the specific SNPs on the gene to perform prioritization. If users have a specified SNP or a list of SNP rsid's needs to be prioritized, they can use Query by SNP option and upload the SNP list in an Excel-format file. Finally, if users have a novel SNP sequence, FASTSNP provides Novel SNP analysis. FASTSNP will generate a SNP Function Report for each SNP. Users can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information.
Proper citation: FastSNP (RRID:SCR_003140) Copy
Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).
Proper citation: PHI-base (RRID:SCR_003331) Copy
One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool
Proper citation: T-profiler (RRID:SCR_003452) Copy
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