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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BLASR Resource Report Resource Website 10+ mentions Discontinued |
BLASR (RRID:SCR_000764) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Proovread |
PMID:22988817 DOI:10.1186/1471-2105-13-23 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:blasr, OMICS_05134 | https://bio.tools/blasr, https://sources.debian.org/src/blasr/ | SCR_000764 | SciCrunch Registry | Basic Local Alignment with Successive Refinement, BLASR: The PacBio long read aligner | 2026-09-26 02:12:51 | 15 | ||||||
|
GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | SciCrunch Registry | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-09-26 02:12:50 | 3 | |||||
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Syndicated Universities Preparatory Research Educational Program Resource Report Resource Website |
Syndicated Universities Preparatory Research Educational Program (RRID:SCR_000768) | data or information resource, organization portal, portal, training resource | SUPREP MODEL LEARNING is a standardized credit earning academic exchange program that enables a student from any third world countries or technologically deficient institutions around the world, to attend and earn credits from the best traditional recognized accredited institutions globally, in which the credits earned are transferred to the home institution or SUPREP agency for aggregation towards successful graduation. :The goal of this program is to facilitate bringing students from the third world to reputable undergraduate and graduate neuroscience programs. Additionally, this program also aims t o grant Third World Neuroscience students Academic exchange programs worldwide. | education, exchange, academic, institution, international, medical, neuroscience, outreach, professional, program, research, student, study abroad, technologically, third world, undergraduate | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24046 | SCR_000768 | SciCrunch Registry | SUPREP | 2026-09-26 02:12:51 | 0 | |||||||||
|
detecttd Resource Report Resource Website |
detecttd (RRID:SCR_000681) | detecttd | software resource | Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone. | tandem duplication, sequencing read, python, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00315 | SCR_000681 | SciCrunch Registry | detecttd - Tool to detect tandem duplications in NGS reads | 2026-09-26 02:12:50 | 0 | |||||||
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FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | SciCrunch Registry | 2026-09-26 02:12:50 | 4 | ||||||||
|
Canadian Online CME Sites Resource Report Resource Website |
Canadian Online CME Sites (RRID:SCR_000683) | Canadian Online CME | continuing medical education, data or information resource, portal, training resource | Annotated list of online CME (continuing medical education) with links to, and descriptions of, Web Sites offering courses and CME credit specifically aimed at Canadian physicians. All Canadian Online CME offering MainPro-M1 credit includes an online group discussion format. You must participate in these discussions as well as go though the didactic material to earn credit. | education, audio, canada, course, credit, mainpro-m1, medical, podcast, slide, video | has parent organization: CMEList.com | nif-0000-23612 | SCR_000683 | SciCrunch Registry | 2026-09-26 02:12:50 | 0 | |||||||||
|
Keyose Resource Report Resource Website |
Keyose (RRID:SCR_000798) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 5, 2014. Keyose is a project designed and led by a family physician. We are not IT focused, but health-care focused. Technology is just a tool, not our purpose. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31988 | http://www.keyose.com | SCR_000798 | SciCrunch Registry | Keyose | 2026-09-26 02:12:52 | 0 | |||||||||
|
clipcrop Resource Report Resource Website |
clipcrop (RRID:SCR_000678) | software resource | Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files. | structural variation, detecting structural variations, soft-clipping information, SAM files, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22373054 | Free, Available for download, Freely available | biotools:clipcrop, OMICS_00310 | https://bio.tools/clipcrop | SCR_000678 | SciCrunch Registry | ClipCrop | 2026-09-26 02:12:50 | 0 | ||||||
|
TriageTools Resource Report Resource Website |
TriageTools (RRID:SCR_000675) | TriageTools | software resource | A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. | matlab, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23408855 | Free, Available for download, Freely available | biotools:triagetools, nlx_156740 | https://bio.tools/triagetools | SCR_000675 | SciCrunch Registry | 2026-09-26 02:12:50 | 0 | ||||||
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Clinical Trials Registry - India Resource Report Resource Website 10+ mentions |
Clinical Trials Registry - India (RRID:SCR_000679) | CTRI | clinical trial, data or information resource, data repository, database, service resource, storage service resource | Free, online public record system for registration of clinical trials being conducted in India. Initiated as a voluntary measure, trial registration in the CTRI has been made mandatory by the Drugs Controller General (India) (DCGI) (http://www.cdsco.nic.in/). Moreover, Editors of Biomedical Journals of 11 major journals of India declared that only registered trials would be considered for publication. Today, any researcher who plans to conduct a trial involving human participants, of any intervention such as drugs, surgical procedures, preventive measures, lifestyle modifications, devices, educational or behavioral treatment, rehabilitation strategies as well as trials being conducted in the purview of the Department of AYUSH (http://indianmedicine.nic.in/) is expected to register the trial in the CTRI before enrollment of the first participant. Trial registration involves public declaration and identification of trial investigators, sponsors, interventions, patient population etc before the enrollment of the first patient. Submission of Ethics approval and DCGI approval (if applicable) is essential for trial registration in the CTRI. Multi-country trials, where India is a participating country, which have been registered in an international registry, are also expected to be registered in the CTRI. In the CTRI, details of Indian investigators, trial sites, Indian target sample size and date of enrollment are captured. After a trial is registered, trialists are expected to regularly update the trial status or other aspects as the case may be. After a trial is registered, all updates and changes will be recorded and available for public display. The CTRI is working with the WHO ICTRP to ensure that results of all trials registered with the CTRI are adequately reported and publicly available. | clinical trial, registry, registration, trial, clinical, randomized, non-randomized, india |
is listed by: WHO International Clinical Trials Registry Platform has parent organization: National Institute of Medical Statistics; New Delhi; India |
PMID:18630235 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100010980, nlx_151507 | https://doi.org/10.17616/R3C61N | SCR_000679 | SciCrunch Registry | Clinical Trials Registry-India (CTRI), Clinical Trials Registry-India, Clinical Trials Registry - India (CTRI) | 2026-09-26 02:12:50 | 13 | |||||
|
VarB Resource Report Resource Website |
VarB (RRID:SCR_000671) | VarB | software resource | A variation browsing and analysis tool for variants derived from next-generation sequencing data. | variant, next-generation sequencing, polymorphism, c++ | is listed by: OMICtools | PMID:22976080 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00898 | SCR_000671 | SciCrunch Registry | 2026-09-26 02:12:50 | 0 | |||||||
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ROSTLAB Resource Report Resource Website 1+ mentions |
ROSTLAB (RRID:SCR_000792) | group | A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. | protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical |
has parent organization: Columbia University; New York; USA is parent organization of: PredictNLS is parent organization of: SNPdbe |
NLM LM007329; NLM GM50291 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31417 | http://cubic.bioc.columbia.edu/services/disis | SCR_000792 | SciCrunch Registry | Rost Group | 2026-09-26 02:12:52 | 1 | ||||||
|
BAMseek Resource Report Resource Website |
BAMseek (RRID:SCR_000672) | BAMseek | data processing software, data visualization software, software application, software resource | A Large File Viewer for BAM and SAM alignment files. | matlab, sam, bam, viewer, alignment, format, large file, vcf, sff, fastq, sequencing |
is listed by: OMICtools has parent organization: Google Code |
Free, Available for download, Freely available | OMICS_00877 | SCR_000672 | SciCrunch Registry | bamseek - Browse large BAM and SAM alignment files. | 2026-09-26 02:12:50 | 0 | |||||||
|
Virginia Commonwealth University, Department of Pharmacology Resource Report Resource Website |
Virginia Commonwealth University, Department of Pharmacology (RRID:SCR_000666) | university | A graduate program for pharmacology and toxicology that is a component of the Virginia Commonwealth University. This organization also performs studies on medical disorders, and new pharmacology agents and their effects on human health. | pharmacology, toxicology, virginia commonwealth, medical disorders, graduate program, pharmacology agents | has parent organization: Virginia Commonwealth University; Virginia; USA | nif-0000-02004 | http://views.vcu.edu/pharmtox/ | SCR_000666 | SciCrunch Registry | VCU SOM Pharmacology and Toxicology, VCU Department of Pharmacology and Toxicology, VCU Pharmacology and Toxicology, VCU Department of Pharmacology Toxicology, VCU School of Medicine; Department of Pharmacology and Toxicology | 2026-09-26 02:12:50 | 0 | ||||||||
|
Functional Annotation of the Mammalian Genome Resource Report Resource Website 10+ mentions |
Functional Annotation of the Mammalian Genome (RRID:SCR_000788) | FANTOM | consortium, data or information resource, database, organization portal, portal | International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN. | mammal, genome, isoform, human, gene, transcriptome, regulatory network, FASEB list |
is related to: CAGE Basic Viewer for Mus musculus is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
NIMH MH062261 | PMID:20211142 PMID:33211864 |
nif-0000-30552 | http://fantom.gsc.riken.jp | SCR_000788 | SciCrunch Registry | Functional Annotation of the Mammalian Genome, FANTOM, Functional Annotation of the Mammalian Genome (FANTOM) | 2026-09-26 02:12:51 | 43 | |||||
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NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01063 | SCR_000664 | SciCrunch Registry | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2026-09-26 02:12:50 | 3 | |||||||
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Opera Resource Report Resource Website 1+ mentions |
Opera (RRID:SCR_000665) | software resource | A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads. | sequence assembly, paired-end, orient contigs, shotgun-sequencing, shotgun, software program, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:27169502 PMID:21929371 |
Free, Available for download, Freely available | biotools:opera, OMICS_00045 | https://bio.tools/opera | SCR_000665 | SciCrunch Registry | OPERA-LG, Optimal Paired-End Read Assembler | 2026-09-26 02:12:50 | 3 | ||||||
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FAS Center For Systems Biology Resource Report Resource Website 1+ mentions |
FAS Center For Systems Biology (RRID:SCR_000789) | group | A group dedicated to combining a variety of experimental and theoretical approaches to find general principles that explain the structure, behavior and evolution of cells and organisms. The center hosts a variety of fellows and faculty from various backgrounds such as biology, physics, chemistry, mathematics, computer science and engineering. | cell, organism, evolution, biology, physics, chemistry, mathematics, computer science, engineering, hybridization | has parent organization: Harvard University; Cambridge; United States | National Science Foundation DEB 0415718; National Science Foundation DEB 0640512 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30555 | SCR_000789 | SciCrunch Registry | FAS Center | 2026-09-26 02:12:52 | 2 | |||||||
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Semantic Web Applications in Neuromedicine (SWAN) Ontology Resource Report Resource Website |
Semantic Web Applications in Neuromedicine (SWAN) Ontology (RRID:SCR_000697) | SWAN Ontology | controlled vocabulary, data or information resource, narrative resource, ontology | The SWAN (Semantic Web Applications in Neuromedicine) ontology is an ontology for modeling scientific discourse and has been developed in the context of building a series of applications for biomedical researchers, as well as extensive discussions and collaborations with the larger bio-ontologies community. Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. The SWAN ontology is organized in three types of modules: * basic: basic modules represent the ontology building blocks. They cover topics that are general enough to be included in every ontology distribution. The current basic modules are: ** collections ** provenance, authoring and versioning (PAV) ** discourse relationships ** FOAF (in OWL-DL) ** SKOS (in OWL-DL) ** qualifiers ** scientific discourse * extension: extensions modules are covering topics (a) that can be related only to some fields of science (b) for which there could be more than one implementation (c) for which a temporary solution has been provided and it is possible to forecast its substitution. The current extensions modules are: ** life science entities ** citations ** qualifiers extension modules * distribution: distributions are modules that are including all the basic modules and extensions necessary for serving a specific domain (i.e. the SWAN ontology for the Alzheimer knowledge base or the generic distribution that is not binded to any specific scientific domain). The current available distributions are: ** swan-scientific-discourse ** swan-alzheimer | scientific discourse, biomedical research, semantics, owl, semantic web, biomedicine, swan, alzheimer disease, knowledgebase, hypothesis/claim-based representation of the rhetorical structure of a scientific paper |
is listed by: FORCE11 is related to: AlzSWAN Knowledge Base has parent organization: Harvard Medical School; Massachusetts; USA |
Ellison Medical Foundation ; alz.org ; Eli Lilly and Company |
PMID:18583197 | nlx_149502 | SCR_000697 | SciCrunch Registry | Semantic Web Applications in Neuromedicine Ontology | 2026-09-26 02:12:50 | 0 | ||||||
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PiNGO Resource Report Resource Website |
PiNGO (RRID:SCR_000692) | PiNGO | software resource | A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotation, network, candidate gene, biological network, ontology or annotation search engine, statistical analysis, term enrichment, functional similarity, functional prediction, search engine, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:21278188 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149330, OMICS_02281 | SCR_000692 | SciCrunch Registry | 2026-09-26 02:12:50 | 0 |
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