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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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FlyMine Resource Report Resource Website 100+ mentions |
FlyMine (RRID:SCR_002694) | FlyMine | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API | anopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publication, FASEB list |
is related to: FlyBase is related to: UniProt is related to: Ensembl is related to: InterPro is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Tree families database is related to: IntAct is related to: Gene Ontology is related to: GOA is related to: ArrayExpress is related to: REDfly Regulatory Element Database for Drosophilia is related to: KEGG is related to: Reactome has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust 067205; NHGRI |
PMID:17615057 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02845 | SCR_002694 | 2026-08-10 09:31:48 | 107 | ||||||
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SuperPred: Drug classification and target prediction Resource Report Resource Website 10+ mentions |
SuperPred: Drug classification and target prediction (RRID:SCR_002691) | SuperPred | data or information resource, database, web service, software resource, data access protocol | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits. | drug, drug class, drug target, addiction, anatomical therapeutic chemical, application area, biological activity, chemical, chemical classification, chemical property, classification, compound, molecular target, molecule, nervous system, pathway, pharmacological property, physicochemical property, prediction, activity spectra, substance, structural similarity, structure, tanimoto coefficient, tanimoto score, target prediction, target-prediction server, therapeutic approach, therapeutic property, drug classification, target prediction, similarity score, target, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
SFB 449 ; IRTG Berlin-Boston-Kyoto and Deutsche Krebshilfe. ; DFG |
PMID:18499712 PMID:24878925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:superpred, nif-0000-00415 | https://bio.tools/superpred | SCR_002691 | 2026-08-10 09:31:48 | 10 | |||||
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rsync Resource Report Resource Website 1+ mentions |
rsync (RRID:SCR_003113) | source code, software resource | Software that provides rapid incremental file transfer. | file transfer |
is used by: studyforrest.org has parent organization: Samba |
Free, Available for download, Freely available | nlx_156711 | SCR_003113 | 2026-08-09 09:03:41 | 7 | |||||||||
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MF-GE Resource Report Resource Website |
MF-GE (RRID:SCR_003509) | MF-GE | source code, software resource | A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map. | microarray, classification, gene |
is listed by: OMICtools has parent organization: University of Sydney; Sydney; Australia |
PMID:20122224 | OMICS_02295 | SCR_003509 | Multiple Filters enhanced Genetic Ensemble System (MF-GE), Multiple Filters enhanced Genetic Ensemble System | 2026-08-09 09:03:48 | 0 | |||||||
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Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra Resource Report Resource Website |
Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra (RRID:SCR_004315) | source code, software resource | Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra. | has parent organization: University of Washington; Seattle; USA | PMID:16447975 | nlx_32529 | SCR_004315 | ChargeCzar, Charge Czar | 2026-08-09 09:03:54 | 0 | |||||||||
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Segtools Resource Report Resource Website 1+ mentions |
Segtools (RRID:SCR_004394) | source code, software resource | Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another. | has parent organization: University of Washington; Seattle; USA | PMID:22029426 | nlx_40271 | SCR_004394 | 2026-08-09 09:03:55 | 5 | ||||||||||
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CPODES numerical integrator Resource Report Resource Website 1+ mentions |
CPODES numerical integrator (RRID:SCR_000766) | CPODES | source code, software resource | CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules. | dynamic, numerical integrator, multibody, source code |
uses: Simbody(tm): SimTK Multibody Dynamics Toolset is listed by: Simtk.org |
Free, Available for download, Freely available | nif-0000-23329 | SCR_000766 | 2026-08-09 09:03:02 | 6 | ||||||||
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BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | source code, software resource | A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub. | bam, next-generation sequencing, java, snp calling, structural annotation, macosx, unix, windows, visualize, analyze, sequence read, reference sequence, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22253280 PMID:20071372 |
GNU General Public License | biotools:bamview, OMICS_00878, nlx_22933 | https://bio.tools/bamview | SCR_004207 | 2026-08-09 09:03:51 | 21 | ||||||
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Commons In A Box Resource Report Resource Website |
Commons In A Box (RRID:SCR_002620) | CBOX | source code, software resource | A free, distributable, easy-to-install software package of customizable, WordPress-based commons spaces for communities. This software project aimed at turning the infrastructure that successfully powers the CUNY (City University of New York) Academic Commons takes the complexity out of creating a Commons site, helping organizations create a space where their members can discuss issues, collaborate on projects, and share their work. CBOX also provides: * Out-of-the-box functionality with an intuitive set-up that guides site administrators through each step of installation. * A powerful, responsive, highly customizable theme developed for community engagement, based on PressCrew's Infinity Theming Engine. * Responsive design for easy viewing on many devices, including tablets and smartphones. * Collaborative document creation and file sharing. * Reply-By-Email functionality for quick, on-the-go communication. * Compatibility with many other WordPress and BuddyPress themes and plug-ins. * Expansive wiki options. CBOX will be useful to any organization that is looking for a shared space in which to build an engaged community of users and developers. Download their code, peruse their documentation, check out their project demo website, and join their community to find others using CBOX. | process, wordpress, commons, community, community building portal |
is listed by: FORCE11 is related to: WordPress has parent organization: City University of New York; New York; USA |
Alfred P. Sloan Foundation | Free, Available for download, Freely available | nlx_156036 | http://www.force11.org/node/4697 | SCR_002620 | 2026-08-09 09:03:30 | 0 | ||||||
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Fascinator Resource Report Resource Website |
Fascinator (RRID:SCR_001367) | source code, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An extensible, open-source platform for managing your digital objects. Using a variety of plugins, you can transform your digital objects into new formats, search and browse through your collection, collaborate through tagging and annotations, and create packages of information for publishing to all manner of systems. Written in Python. | open source, digital objects, format, annotation, tagging, python | has parent organization: University of Southern Queensland; Queensland; Australia | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-07756 | SCR_001367 | The Fascinator | 2026-08-09 09:03:09 | 0 | ||||||||
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Genomedata Resource Report Resource Website 1+ mentions |
Genomedata (RRID:SCR_004544) | Genomedata | source code, software resource | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-08-09 09:03:55 | 1 | ||||||
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RNAplex Resource Report Resource Website 10+ mentions |
RNAplex (RRID:SCR_002763) | RNAplex | source code, software resource | Software tool to rapidly search for short interactions between two long RNAs. | interaction, rna, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Leipzig; Saxony; Germany |
PMID:21593134 PMID:18434344 |
Free, Freely available, Available for download | rid_000107, biotools:rnaplex | https://bio.tools/rnaplex | SCR_002763 | 2026-08-09 09:03:35 | 37 | ||||||
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Time-resolved and time-scale adaptive measures of spike train synchrony Resource Report Resource Website 1+ mentions |
Time-resolved and time-scale adaptive measures of spike train synchrony (RRID:SCR_001667) | Time-resolved and time-scale adaptive measures of spike train synchrony | source code, software resource | Source code that allows you to calculate the different measures used in Kreuz T, Chicharro D, Greschner M, Andrzejak RG (2011): Time-resolved and time-scale adaptive measures of spike train synchrony, http://www.sciencedirect.com/science/article/pii/S0165027010006564. Journal of Neuroscience Methods,195, 92-106 & Kreuz T, Chicharro D, Andrzejak RG, Haas JS, and Abarbanel HDI (2009) Measuring multiple spike train synchrony. Journal of Neuroscience Methods 183:287-299 http://www.sciencedirect.com/science/article/pii/S0165027009003616 | synchrony, spike train, time series analysis, synchronization, clustering, neuronal coding | has parent organization: Pompeu Fabra University; Barcelona; Spain | Marie Curie Individual Outgoing Fellowship ; Spanish Ministry of Education and Science BFU2007-61710; European Social Fund 2008FI-B 00460 |
PMID:21129402 PMID:19591867 |
Free, Freely Available | nlx_153991 | SCR_001667 | 2026-08-09 09:03:14 | 1 | ||||||
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Visual Molecular Dynamics Resource Report Resource Website 100+ mentions |
Visual Molecular Dynamics (RRID:SCR_001820) | VMD | source code, software resource | A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. | standalone software, mac os x, unix, virtual machine, windows, c++ |
is listed by: OMICtools has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS | PMID:8744570 | Free, Freely available | OMICS_03804 | SCR_001820 | 2026-08-09 09:03:17 | 383 | ||||||
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Reliable detection of directional couplings using rank statistics Resource Report Resource Website 1+ mentions |
Reliable detection of directional couplings using rank statistics (RRID:SCR_001662) | Reliable detection of directional couplings using rank statistics | source code, software resource | Source code that allows you to calculate the different measures used in Chicharro D, Andrzejak RG (2009): Reliable detection of directional couplings using rank statistics. Physical Review E, 80, 026217. | directional coupling, time series, rank statistics, normalization, experimental signal | has parent organization: Pompeu Fabra University; Barcelona; Spain | PMID:19792241 | Free, Freely Available | nlx_153987 | SCR_001662 | 2026-08-09 09:03:18 | 1 | |||||||
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XP-CLR Resource Report Resource Website 50+ mentions |
XP-CLR (RRID:SCR_004961) | source code, software resource | XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available. | has parent organization: Harvard Medical School; Massachusetts; USA | Restricted | nlx_94751 | https://reich.hms.harvard.edu/software | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004961 | XP-CLR Software | 2026-08-09 09:04:04 | 74 | |||||||
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D2R Server - Publishing Relational Databases on the Semantic Web Resource Report Resource Website |
D2R Server - Publishing Relational Databases on the Semantic Web (RRID:SCR_004963) | D2R Server | source code, software resource | D2R Server is a tool for publishing relational databases on the Semantic Web. It enables RDF and HTML browsers to navigate the content of the database, and allows applications to query the database using the SPARQL query language. Data on the Semantic Web is modeled and represented in RDF. D2R Server uses a customizable D2RQ mapping to map database content into this format, and allows the RDF data to be browsed and searched the two main access paradigms to the Semantic Web. D2R Server''s Linked Data interface makes RDF descriptions of individual resources available over the HTTP protocol. An RDF description can be retrieved simply by accessing the resource''s URI over the Web. Using a Semantic Web browser like Tabulator (slides) or Disco, you can follow links from one resource to the next, surfing the Web of Data. The SPARQL interface enables applications to search and query the database using the SPARQL query language over the SPARQL protocol. Requests from the Web are rewritten into SQL queries via the mapping. This on-the-fly translation allows publishing of RDF from large live databases and eliminates the need for replicating the data into a dedicated RDF triple store. The latest source code is available from the project''s CVS repository and can be browsed online. | has parent organization: Free University of Berlin; Berlin; Germany | nlx_92812 | SCR_004963 | 2026-08-09 09:04:01 | 0 | ||||||||||
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ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | source code, software resource | ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed. | diploid, genotype, snp, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Cornell University; New York; USA |
NSF 0606461 | PMID:20926420 | GNU General Public License | biotools:alchemy, nlx_149227 | https://bio.tools/alchemy | SCR_005761 | ALCHEMY - An automated population genetic model driven SNP genotype calling method | 2026-08-09 09:04:10 | 5 | ||||
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Grid Enabled Molecular Science Through Online Networked Environments Resource Report Resource Website |
Grid Enabled Molecular Science Through Online Networked Environments (RRID:SCR_008629) | GEMSTONE | source code, software resource | Integrated framework for accessing grid resources that supports scientific exploration, workflow capture and replay, and a dynamic services oriented architecture. This framework provides researchers in the molecular sciences with a tool to discover remote grid application services and compose them as appropriate to the chemical and physical nature of the problem at hand. The initial set of application services include molecular quantum and classical chemistries (GAMESS, APBS, Polyrate), along with supporting services for visualization (QMView), databases, auxillary chemistry services, and documentation and education materials. * Rich-client Desktop Interface - Gemstone is a Firefox extension that provides a dynamic user interface to backend computational, data and visualization services. * Workflow Integration - Gemstone supports a workflow component based on Informnet (see http://grid-devel.sdsc.edu/informnet). They are adapting the Informnet workflow engine to support workflow publication and discovery, brokering, and fault tolerance. They are also adding support for automatic generation of workflows based on user interaction. * Strongy Typed Data Schemas - They are working extensively with CML, integrating their data schemas into workflow systems and providing bridges to the GamesXML that they defined. |
has parent organization: University of California at San Diego; California; USA has parent organization: National Biomedical Computation Resource has parent organization: University of Zurich; Zurich; Switzerland |
Mozilla Foundation ; Pioneers of the Inevitable ; Oregon State University; Oregon; USA ; Open Source Lab ; strg.at ; Google ; Mozdev Group Inc ; enQuira ; Webspam.org ; Web Hosting Search |
nif-0000-32004 | SCR_008629 | 2026-08-09 09:04:59 | 0 | |||||||||
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Gene Ontology Browsing Utility (GOBU) Resource Report Resource Website |
Gene Ontology Browsing Utility (GOBU) (RRID:SCR_005662) | GOBU | source code, software resource | Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, gene, browser, computation, visualization, software library, statistical analysis, term enrichment, ontology or annotation browser, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Academia Sinica; Taipei; Taiwan |
Open unspecified license - Free for academic use | nlx_149098 | SCR_005662 | Gene Ontology Browsing Utility | 2026-08-09 09:04:13 | 0 |
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