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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FastSemSim Resource Report Resource Website 1+ mentions |
FastSemSim (RRID:SCR_006919) | FastSemSim | software toolkit, software resource, software library | A package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, functional similarity, semantic similarity, graphical user interface, gene ontology, annotation, parse, gene, protein |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Padua; Padua; Italy has parent organization: SourceForge |
Open unspecified license - Free for academic use. GNU GPL license. However, This software is currently unpublished work. You must contact us before using it or its results or any work/app. based on top of it in any published work. | nlx_149309 | SCR_006919 | 2026-08-04 09:41:42 | 6 | ||||||||
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BMDExpress Resource Report Resource Website 10+ mentions |
BMDExpress (RRID:SCR_006823) | BMDExpress | data processing software, software application, software resource, data analysis software | Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments. | bioinformatics, microarray, software, toxicogenomics |
is related to: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry has parent organization: SourceForge |
MIT License | nlx_152743 | SCR_006823 | 2026-08-04 09:41:42 | 32 | ||||||||
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Adverse Event Ontology Resource Report Resource Website |
Adverse Event Ontology (RRID:SCR_006807) | AEO | ontology, data or information resource, controlled vocabulary | AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms | has parent organization: SourceForge | nlx_44108 | SCR_006807 | 2026-08-04 09:41:42 | 0 | ||||||||||
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Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | data analysis service, source code, analysis service resource, software resource, production service resource, service resource, database, data or information resource | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | 2026-08-04 09:41:31 | 0 | |||||
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BLESS Resource Report Resource Website 10+ mentions |
BLESS (RRID:SCR_005963) | BLESS | data processing software, data analysis software, algorithm resource, software resource, sequence analysis software, software application | Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory. | c++, next-generation sequencing, bloom-filter, error correction, ngs, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24451628 | GNU General Public License v3 | OMICS_02246, biotools:bless | https://bio.tools/bless | SCR_005963 | BLoom-filter-based Error correction Solution for high-throughput Sequencing reads, BLESS - Bloom-filter-based Error Correction Tool for NGS reads | 2026-08-04 09:41:28 | 45 | |||||
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Centroid Trajectory Analysis Resource Report Resource Website 10+ mentions |
Centroid Trajectory Analysis (RRID:SCR_006331) | CeTrAn | data processing software, software application, software resource, data analysis software | Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file. | trajectory, buridan, principal components analysis, correlation analysis, buridan's paradigm, locomotion, software, tracking, drosophila |
has parent organization: Free University of Berlin; Berlin; Germany has parent organization: SourceForge |
Swiss National Science Foundation PA00P3_124141; EPSRC EP/F030673/1 |
PMID:22912692 | Open source, Available for Mac and PC, Source code available for download | nlx_152033 | SCR_006331 | CeTrAn: centroid trajectory analysis | 2026-08-04 09:41:34 | 11 | |||||
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go-moose Resource Report Resource Website |
go-moose (RRID:SCR_005666) | go-moose | data processing software, software application, software resource, data analysis software | go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, slimmer-type tool, analysis, gene ontology, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: go-perl is related to: go-db-perl has parent organization: SourceForge has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: Lawrence Berkeley National Laboratory |
Free for academic use | nlx_149189 | SCR_005666 | 2026-08-04 09:41:24 | 0 | ||||||||
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Brain Networks Resource Report Resource Website 1+ mentions |
Brain Networks (RRID:SCR_005841) | Brain Networks | data processing software, source code, data analysis software, software resource, software application | Brain Networks: Code to perform network analysis on brain imaging data. | brain, imaging, network analysis, brain imaging, neuroimaging | has parent organization: SourceForge | PMID:21031030 | Open unspecified license - GNU General Public License (GPL) | nlx_149364 | SCR_005841 | brainnetworks | 2026-08-04 09:41:27 | 1 | ||||||
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ESTScan Resource Report Resource Website 100+ mentions |
ESTScan (RRID:SCR_005742) | ESTScan | data processing software, software application, software resource, data analysis software | ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics. | dna, dna sequence, coding region, perl module, c, btlib perl module |
is listed by: Debian is listed by: OMICtools has parent organization: SourceForge |
PMID:10786296 | OMICS_08423, nlx_149202 | https://sources.debian.org/src/estscan/ | SCR_005742 | ESTScan project | 2026-08-04 09:41:26 | 289 | ||||||
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SPInDel Resource Report Resource Website 1+ mentions |
SPInDel (RRID:SCR_004509) | SPInDel | data set, software resource, data or information resource | A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species. | virus, indel, dna barcoding, alignment, nucleotide sequence, visualization, conserved region, pcr primer, phylogenetic, variant |
is listed by: OMICtools has parent organization: University of Porto; Porto; Portugal has parent organization: SourceForge |
PMID:22978681 PMID:20923781 |
Acknowledgement requested, Free, Public | OMICS_01496 | SCR_004509 | SPecies Identification by Insertions/Deletions, SPInDel - Species identification by insertions/deletions | 2026-08-04 09:41:09 | 2 | ||||||
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iso2mesh Resource Report Resource Website 10+ mentions |
iso2mesh (RRID:SCR_013202) | iso2mesh | software application, software resource, software toolkit | A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling. | matlab, mesh generation, modeling, magnetic resonance, optical imaging, os independent, mri, computed tomography, octave |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155855 | http://www.nitrc.org/projects/iso2mesh | SCR_013202 | 2026-08-04 09:43:09 | 25 | |||||||
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PerlPrimer Resource Report Resource Website 100+ mentions |
PerlPrimer (RRID:SCR_012038) | software application, software resource | A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:15073005 DOI:10.1093/bioinformatics/bth254 |
Open unspecified license | OMICS_02354 | https://sources.debian.org/src/perlprimer/ | SCR_012038 | PerlPrimer - open-source PCR primer design | 2026-08-04 09:42:54 | 236 | |||||||
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OLORIN Resource Report Resource Website |
OLORIN (RRID:SCR_002015) | OLORIN | software application, software resource | An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, any platform with java 1.6 or later, next generation sequencing, variant, haplotype, allele frequency, java swing |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: SourceForge |
PMID:23052039 | Free, Available for download, Freely available | nlx_154503, OMICS_01556 | http://sourceforge.net/p/olorin/ | SCR_002015 | 2026-08-04 09:40:32 | 0 | ||||||
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HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software application, software resource | A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:15377505 | Free, Freely Available | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2026-08-04 09:40:27 | 45 | |||||
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MetAssign Resource Report Resource Website 1+ mentions |
MetAssign (RRID:SCR_000092) | software application, standalone software, software resource | Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download. | peak annotation, peaks probabilistic identifications, |
is listed by: OMICtools is listed by: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:24916385 | Free, Available for download, Freely available | OMICS_04679 | http://mzmatch.sourceforge.net/ | SCR_000092 | 2026-08-04 09:40:03 | 1 | |||||||
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NGS-Cleaner Resource Report Resource Website |
NGS-Cleaner (RRID:SCR_000574) | NGS-Cleaner | software application, software resource | Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available, | OMICS_01166 | SCR_000574 | 2026-08-04 09:40:10 | 0 | ||||||||
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Object-Oriented Development Interface for NMR Resource Report Resource Website 10+ mentions |
Object-Oriented Development Interface for NMR (RRID:SCR_005974) | ODIN | software application, software resource | A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms. | analyze, c++, console (text based), dicom, image display, image reconstruction, modeling, magnetic resonance, nifti, os independent, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: SourceForge |
GNU General Public License | nlx_155909 | https://sources.debian.org/src/odin/ | SCR_005974 | Object Oriented Development Interface for NMR, ODIN - Object-Oriented Development Interface for NMR | 2026-08-04 09:41:29 | 15 | ||||||
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(at)Note Resource Report Resource Website 1+ mentions |
(at)Note (RRID:SCR_005342) | (at)Note | software application, software resource, text-mining software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 18, 2017. Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels. | java, java swt, text, mining |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Minho; Braga; Portugal |
PMID:19393341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01167 | SCR_005342 | (at)Note2 - A workbench for Biomedical Text Mining | 2026-08-04 09:41:20 | 2 | ||||||
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Mesh-based Monte Carlo (MMC) Resource Report Resource Website |
Mesh-based Monte Carlo (MMC) (RRID:SCR_006950) | MMC | software application, software resource | A Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MMC or tMCimg), MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smooth/complex boundaries, but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores. | c, console (text based), modeling, monte carlo, optical imaging, posix/unix-like |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155810 | http://www.nitrc.org/projects/mmc | SCR_006950 | Mesh-based Monte Carlo | 2026-08-04 09:41:43 | 0 | ||||||
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BioMail Resource Report Resource Website 1+ mentions |
BioMail (RRID:SCR_008174) | software application, software resource | BioMail is a small web-based application for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is written to automate searching for recent scientific papers in the PubMed Medline database. BioMail is free and will stay free. What does BioMail do? Periodically BioMail does a user-customized Medline search and sends all matching articles recently added to Medline to the users'' e-mail address. HTML-formatted e-mails generated by BioMail can be used to view selected references in medline format (compatible with most reference manager programs). Why is BioMail helpful? If you use Medline, it may be hard to remember when you did your last search. Often you must scan titles you have already seen to be certain you didn''t miss an important reference. BioMail will perform routine searches for you. This program alerts users to all new papers in their fields automatically. It also helps the user to ''refine'' search patterns once and for all. There is no need to wonder: ''What was that great search pattern I used last Saturday?''. All patterns are safe in the database and can be accessed, tuned, or deleted any time. It is also useful for countries where access to the Internet is not yet widely available. If a person has a permanent e-mail address, but only sporadic www access, she/he only needs to fill out a BioMail form once and then will receive new references from Medline continually. | articles, journals, medline interface | has parent organization: SourceForge | nif-0000-21059 | SCR_008174 | BioMail | 2026-08-04 09:42:03 | 1 |
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