Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Bycom Resource Report Resource Website |
Bycom (RRID:SCR_000659) | software resource | A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output. | methylcytosine, bs-seq, fastq, sam, bam, snps, snp, wgbs, rrbs, sorftw |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25255082 | Free, Available for download, Freely available | OMICS_00594 | SCR_000659 | 2026-07-25 12:10:24 | 0 | ||||||||
|
BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | software resource, source code | 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 | 2026-07-25 12:13:22 | 21 | ||||||
|
ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | software resource, source code | 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 | 2026-07-25 12:13:24 | 5 | ||||
|
OWL API Resource Report Resource Website 10+ mentions |
OWL API (RRID:SCR_005734) | OWL API | software resource, source code | The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, owl, api, java, software library, parser, writer |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: SourceForge |
Open unspecified license - Free for academic use; available under either the LGPL or Apache Licenses | nlx_149195 | SCR_005734 | The OWL API, OWLAPI | 2026-07-25 12:13:24 | 15 | |||||||
|
Neurofitter Resource Report Resource Website 1+ mentions |
Neurofitter (RRID:SCR_005843) | Neurofitter | software resource, source code | Neurofitter is software for parameter tuning of electrophysiological neuron models. It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuron simulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm Optimization, Evolutionary Strategies, etc. | neuron, parameter, tuning, electrophysiology, model, neuron simulator, neuron model |
has parent organization: SourceForge has parent organization: University of Antwerp; Antwerp; Belgium has parent organization: Brandeis University; Massachusetts; USA has parent organization: Okinawa Institute of Science and Technology |
Okinawa Institute of Science and Technology | PMID:18974796 | GNU General Public License, v2 | nlx_149366 | SCR_005843 | 2026-07-25 12:13:24 | 1 | ||||||
|
OrChem Resource Report Resource Website 1+ mentions |
OrChem (RRID:SCR_008865) | OrChem | software resource, source code | OrChem is an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today''s powerful database servers to provide fast response times in equally large data sets. OrChem is an Oracle chemistry plug-in using the Chemistry Development Kit (CDK). The CDK is an open source Java library for Chemoinformatics and Bioinformatics. OrChem is maintained by the chemoinformatics and metabolism team of the European Bioinformatics Institute. Oracle Data cartridges extend the capabilities of the Oracle server. For chemistry various commercial cartridges exist that facilitate searching and analyzing chemical data. OrChem also provides functionality like this, but is not a cartridge. It doesn''t need Oracle''s extensibility architecture because its Java components run as Java stored procedures inside the Oracle standard JVM (Aurora). OrChem is suitable for Oracle 11G and onwards. Starting with Oracle 11g release 1 (11.1) there is a just-in-time(JIT) compiler for Oracle JVM environment. A JIT compiler for Oracle JVM enables much faster execution because it manages the invalidation, recompilation, and storage of code without an external mechanism. This new Oracle feature makes Java classes perform better than before. | oracle, chemistry, cdk, similarity search, chemical structure, cheminformatics, bioinformatics, plugin |
is listed by: 3DVC has parent organization: SourceForge has parent organization: European Bioinformatics Institute |
PMID:20298521 | GNU Lesser General Public License | nlx_149252 | SCR_008865 | 2026-07-25 12:13:26 | 1 | |||||||
|
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 | 2026-07-26 09:05:51 | 25 | |||||||
|
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 | 2026-07-26 09:05:37 | 236 | |||||||
|
MetAssign Resource Report Resource Website 1+ mentions |
MetAssign (RRID:SCR_000092) | software application, software resource, standalone software | 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 | 2026-07-26 09:02:43 | 1 | |||||||
|
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 | 2026-07-26 09:02:50 | 0 | ||||||||
|
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 | 2026-07-26 09:03:12 | 0 | ||||||
|
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 | 2026-07-26 09:03:03 | 45 | |||||
|
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 | 2026-07-26 09:04:04 | 15 | ||||||
|
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 | 2026-07-26 09:04:19 | 0 | ||||||
|
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 | 2026-07-26 09:04:35 | 1 | |||||||||
|
MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | software application, software resource, data processing software | Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer. | parallel computation 4, high-throughput sequencing, sequence alignment, dna, graphics processing unit |
is listed by: OMICtools is related to: MUMmer has parent organization: SourceForge has parent organization: University of Maryland; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873 |
PMID:20161021 | Free, Available for download, Freely available | OMICS_02151 | SCR_001200 | High-throughput sequence alignment using Graphics Processing Units | 2026-07-26 09:03:00 | 5 | |||||
|
skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | software application, software resource, data processing software | Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences. | illumina, unix/linux, c++, adapter trimming, paired-end, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24925680 | Free, Available for download, Freely available | OMICS_02106, biotools:skewer | https://bio.tools/skewer, https://sources.debian.org/src/skewer/, https://github.com/relipmoc/skewer | SCR_001151 | skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences | 2026-07-26 09:03:01 | 11 | |||||
|
UnoSeq Resource Report Resource Website 1+ mentions |
UnoSeq (RRID:SCR_005116) | UnoSeq | software library, software resource, software toolkit | A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists. | java, expression profile, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20194116 | OMICS_01296 | SCR_005116 | UnoSeq - Expression profiling with next generation sequencing without a reference genome | 2026-07-27 09:32:12 | 1 | |||||||
|
SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | service resource, data analysis service, analysis service resource, software resource, production service resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-07-27 09:32:13 | 2 | ||||||
|
PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | service resource, database, software resource, storage service resource, data repository, data or information resource | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-07-27 09:32:16 | 32 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on nidm-terms then you can log in from here to get additional features in nidm-terms such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into nidm-terms you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
