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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Parametric Time Warping Resource Report Resource Website |
Parametric Time Warping (RRID:SCR_003053) | ptw | software resource | Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:14719890 | Free, Freely available | OMICS_02392 | SCR_003053 | ptw: Parametric Time Warping | 2026-07-25 12:05:36 | 0 | ||||||
|
Gutentag Resource Report Resource Website |
Gutentag (RRID:SCR_003051) | software resource | An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend. | standalone software, python, django, genetics, sequence |
is listed by: OMICtools has parent organization: Google Code |
PMID:14640709 | Free, Available for download, Freely available | OMICS_02396 | SCR_003051 | gutentag - A genetic sequence database for labs that can be browsed using tags | 2026-07-25 12:05:37 | 0 | |||||||
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PacBioToCA Resource Report Resource Website 10+ mentions |
PacBioToCA (RRID:SCR_003044) | software resource | A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads. | standalone software | is listed by: OMICtools | PMID:22750884 | Free, Available for download, Freely available | OMICS_05093 | https://rhallpb.github.io/Applications/pacBioToCA.html | SCR_003044 | pacBioToCA (error correction via Celera Assembler) | 2026-07-25 12:05:37 | 13 | ||||||
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R-pbutils Resource Report Resource Website |
R-pbutils (RRID:SCR_002995) | software resource | An R software package providing plotting and convenience functions. | software package, r | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05140 | SCR_002995 | 2026-07-25 12:05:36 | 0 | |||||||||
|
Dana-Farber Cancer Institute Resource Report Resource Website 1+ mentions |
Dana-Farber Cancer Institute (RRID:SCR_003040) | DFCI | institution |
Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world. |
child, adult human, pediatric, young human |
has parent organization: Harvard Medical School; Massachusetts; USA is parent organization of: Spotfinder is parent organization of: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is parent organization of: Gene Index Project is parent organization of: CistromeMap is parent organization of: BINOCh is parent organization of: Dana Farber Tissue Bank is parent organization of: CistromeFinder is parent organization of: TM4 is parent organization of: WorfDB is parent organization of: Predictive Networks is parent organization of: RamiGO is parent organization of: DFCI Animal Resources Facility is parent organization of: DFCI Biohazard Containment Core Facility is parent organization of: DFCI Biospecimen Repository Core Facility is parent organization of: DFCI Blais Proteomics Center is parent organization of: DFCI Clinical Research Laboratory is parent organization of: DFCI Survey and Data Management Core is parent organization of: DFCI Flow Cytometry Core Facility is parent organization of: DFCI Medical Arts Core Facility is parent organization of: DFCI Microarray Core Facility is parent organization of: Dana-Farber Cancer Institute Molecular Biology Core Facility is parent organization of: DFCI RNA Interference Screening Facility is parent organization of: DFCI Shannon McCormack Advanced Molecular Diagnostics Laboratory is parent organization of: MAnorm is parent organization of: NPS is parent organization of: DFCI Confocal and Light Microscopy Core Facility is parent organization of: DFCI Monoclonal Antibody Core Facility is parent organization of: Dana-Farber Cancer Institute Labs and Facilities is parent organization of: DFCI Center for Cancer Computational Biology is parent organization of: GeneSigDB is parent organization of: MACS is parent organization of: DGAP |
Cancer | NCI ; Jimmy Fund |
Free, Freely available | Crossref funder ID: 100007886, grid.65499.37, Wikidata: Q1159198, ISNI: 0000 0001 2106 9910, nif-0000-30432 | https://ror.org/02jzgtq86 | SCR_003040 | Dana Farber Cancer Institute, Dana-Farber | 2026-07-25 12:05:37 | 6 | ||||
|
EnablingOpenScholarship Resource Report Resource Website |
EnablingOpenScholarship (RRID:SCR_003235) | EOS | knowledge environment | An organization for universities and research institutions that is an information service and a forum for raising and discussing issues around the mission of modern universities and research institutions, particularly with regard to the creation, dissemination and preservation of research findings. Its aim is to further the opening up of scholarship and research that we are now seeing through the growing open access, open education, open science and open innovation movements. These, and other, "open" approaches to scholarship are changing the way research and learning are done and there are profound implications for universities and research institutions. EOS has been established to help guide developments and to assist others in understanding the issues and their implications. The context in which EOS has been established is that of increasing interest from governments, funders and the research community itself in opening up the way research is carried out and communicated. This interest is complemented by new research practices and processes that can work effectively only in an open, collaborative environment. Developments of relevance to the mission of EnablingOpenScholarship are reported on and news and details of forthcoming meetings, briefings and discussion sessions is provided. | scholarship, open research, open access |
is listed by: FORCE11 has parent organization: University of Liege; Wallonia; Belgium |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157274 | SCR_003235 | 2026-07-25 12:05:38 | 0 | ||||||||
|
Primer Designer Resource Report Resource Website 1+ mentions |
Primer Designer (RRID:SCR_003189) | Primer Designer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki. | primer, primer design |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02327 | https://www.thermofisher.com/us/en/home/life-science/oligonucleotides-primers-probes-genes/custom-dna-oligos/oligo-design-tools.html?ef_id=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB:G:s&s_kwcid=AL!3652!3!683518170873!e!!g!!primer%20designer!20841448243!155985486683&cid=bid_mol_pch_r01_co_cp1358_pjt0000_bid00000_0se_gaw_nt_pur_con&gad_source=1&gad_campaignid=20841448243&gbraid=0AAAAADxi_GTCU-6xCgQrctnmtmtMSDEQj&gclid=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB | SCR_003189 | 2026-07-25 12:05:37 | 2 | |||||||
|
SALT Resource Report Resource Website 1000+ mentions |
SALT (RRID:SCR_003187) | SALT | software resource | Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families. | next-generation sequencing, protein, protein domain, short read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23782615 | Free, Available for download, Freely available | OMICS_01565, biotools:salt | https://bio.tools/salt | SCR_003187 | SALT - Protein domain classifier | 2026-07-25 12:05:38 | 1294 | |||||
|
XORRO Resource Report Resource Website 1+ mentions |
XORRO (RRID:SCR_003181) | XORRO | software resource | Efficient paired-read overlap software program for use with Illumina sequencing. | illumina, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01569 | SCR_003181 | XORRO: Rapid Paired-End Read Overlapper | 2026-07-25 12:05:38 | 1 | |||||||
|
NovelSeq Resource Report Resource Website |
NovelSeq (RRID:SCR_003136) | NovelSeq | software resource | Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. | sequence, insertion, genome sequencing, genome, next-generation sequencing, illumina, unix, linux, c, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:20385726 | Free, Available for download, Freely available | biotools:novelseq, nlx_156791, OMICS_02164 | https://mybiosoftware.com/novelseq-1-0-2-sequence-insertions-detection.html#google_vignette | SCR_003136 | NovelSeq: Novel Sequence Insertion Detection | 2026-07-25 12:05:37 | 0 | |||||
|
mrCaNaVaR Resource Report Resource Website 10+ mentions |
mrCaNaVaR (RRID:SCR_003135) | mrCaNaVaR | software resource | Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals. | genome, next-generation sequence, duplication, deletion, copy number variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
Free, Freely available | OMICS_02138, nlx_156790, biotools:mrcanavar | https://bio.tools/mrcanavar | SCR_003135 | mrCaNaVaR - micro-read Copy Number Variant Regions, micro-read Copy Number Variant Regions | 2026-07-25 12:05:36 | 14 | ||||||
|
Laura and John Arnold Foundation Resource Report Resource Website 1+ mentions |
Laura and John Arnold Foundation (RRID:SCR_003240) | LJAF | institution | Private foundation whose funding activities are primarily centered around improving life in the United States. Its mission is to produce big and lasting changes in society over the long term. Their four areas of focus (2014) are: criminal justice, K-12 education, public accountability, and research integrity. | grant, criminal justice, k-12 education, public accountability, research integrity | Free, Freely available | Crossref funder ID: 100009827, ISNI: 0000 0004 0555 6315, nlx_157294, grid.480593.3, Wikidata: Q17088752 | https://www.arnoldventures.org/people/laura-arnold-john-arnold | SCR_003240 | Arnold Foundation | 2026-07-25 12:05:39 | 4 | |||||||
|
JCVI Primer Designer Resource Report Resource Website 1+ mentions |
JCVI Primer Designer (RRID:SCR_003275) | JCVI Primer Designer | software resource | High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. | perl, command-line, pcr primer design, pcr, primer, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18405373 | Free, Available for download, Freely available | OMICS_02330 | SCR_003275 | 2026-07-25 12:05:38 | 1 | |||||||
|
SaskPrimerFS Resource Report Resource Website |
SaskPrimerFS (RRID:SCR_003159) | SaskPrimerFS | software resource | Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism. | gene family, pcr primer, pcr, primer, dna sequence, command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02335 | SCR_003159 | 2026-07-25 12:05:38 | 0 | ||||||||
|
GeneCopoeia Resource Report Resource Website 5000+ mentions |
GeneCopoeia (RRID:SCR_003145) | commercial organization | Commercial organization which provides reagents and services for molecular biology research. Its services include clone collections, microRNA solutions, genome editing, qPCR products, and fluorescent labeling and detection. | reagent, pcr, clone, microrna, cell biology | Free, Freely available | nlx_152370 | SCR_003145 | GeneCopoeia Inc | 2026-07-25 12:05:36 | 6981 | |||||||||
|
Pipeliner Resource Report Resource Website 1+ mentions |
Pipeliner (RRID:SCR_003171) | software resource | Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24890372 | Free, Available for download, Freely available | OMICS_04844, biotools:pipeliner | https://bio.tools/pipeliner | SCR_003171 | 2026-07-25 12:05:37 | 6 | |||||||
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Allele Biotechnology Resource Report Resource Website 1+ mentions |
Allele Biotechnology (RRID:SCR_003164) | Allele Biotech | commercial organization | A private company offering a wide variety of Molecular Biology reagents, fluorescent proteins, luciferase assay substrates, genotyping kits, and various custom services. The company isalso in the RNAi field with its recent patents in Pol III promoter-driven siRNA, shRNA, and miRNA. They introduced high titer lentivirus, camelid antibodies, and cell based assays and also offer Baculovirus protein expression and Gryphon retrovirus systems. | molecular biology, reagent, fluorescent protein, luciferase assay substrate, genotyping kit, custom service | is related to: Phoenix | Free, Available for download, Freely available | nlx_156865 | SCR_003164 | Allele Biotechnology and Pharmaceuticals Inc | 2026-07-25 12:05:38 | 1 | |||||||
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American Association for the History of Medicine Resource Report Resource Website |
American Association for the History of Medicine (RRID:SCR_003161) | AAHM | nonprofit organization | A professional association of historians, physicians, nurses, archivists, curators, librarians, and others that promotes and encourages research, study, writing, and interest in the history of medicine and allied fields. | history, medicine | Free, Freely available | nlx_156861, grid.486311.9 | https://ror.org/04w1hax42 | SCR_003161 | 2026-07-25 12:05:37 | 0 | ||||||||
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Relypsa Resource Report Resource Website |
Relypsa (RRID:SCR_004047) | RLYP | commercial organization | Biopharmaceutical company focused on development and commercialization of non-absorbed polymeric drugs to treat disorders in areas of renal, cardiovascular and metabolic diseases.February 2021 - Relypsa changed its name to Vifor Pharma. Company is focused on development and commercialization of late stage medicines that will change treatment paradigms and improve patients lives. | biopharmaceutical, pharmaceutical, drug, late stage medicines, late stage medicines commercialization, late stage medicines development | is related to: Kidney Health Initiative | nlx_158475 | SCR_004047 | Relypsa Inc., Vifor Pharma | 2026-07-25 12:05:46 | 0 | ||||||||
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CADRO Resource Report Resource Website 1+ mentions |
CADRO (RRID:SCR_004046) | CADRO | controlled vocabulary, data or information resource | A classification system developed by the National Institute on Aging and the Alzheimer's Association that can be used to integrate and compare Alzheimer's disease (AD) research portfolios from public and private organizations supporting AD research in the US and abroad. The CADRO was constructed as a three-tier classification system organized around seven major categories: five in research and two resource-related: * Category A. Molecular Pathogenesis and Pathophysiology of Alzheimer's Disease * Category B. Diagnosis, Assessment and Disease Monitoring * Category C. Translational Research and Clinical Interventions * Category D. Epidemiology * Category E. Care, Support and Health Economics of Alzheimer's Diseases * Category F. Research Resources * Category G. Consortia and Public Private Partnerships * Category H. Alzheimer's Disease - Related Dementias Using information from project abstracts and research aims, the above categories were stratified into research topics and these were further divided into research themes. The three levels of classification are meant to enable a fine-grained portfolio analysis that can inform strategic planning and funding decisions. The CADRO was developed as a dynamic portfolio analysis tool that can be used to: (i) capture the changing landscape of AD research funded by different organizations, (ii) identify opportunities for coordination of support for AD research, and (iii) identify funding gaps as well as areas of overlap within and across organizations. | late adult human, alzheimer, aging |
is used by: IADRP has parent organization: Alzheimers Association has parent organization: National Institute on Aging |
Alzheimer's disease, Aging | NIA | nlx_158474 | http://www.nia.nih.gov/research/dn/cadro-outline, http://www.nia.nih.gov/research/dn/common-alzheimers-disease-research-ontology-cadro, http://www.nia.nih.gov/sites/default/files/cadro_outline_-_january_2013.pdf | SCR_004046 | Common Alzheimer''s Disease Research Ontology, Common Alzheimer's Disease Research Ontology (CADRO) | 2026-07-25 12:05:45 | 2 |
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