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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AcroMine Resource Report Resource Website |
AcroMine (RRID:SCR_013196) | software resource, data access protocol, web service, service resource | An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE. | acronym, abbreviation, disambiguation, computational linguistics, text mining |
is listed by: FORCE11 is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
JISC ; BBSRC ; EPSRC |
PMID:20360059 PMID:17050571 |
Free, Public | OMICS_01169, nif-0000-10215 | SCR_013196 | Acromine | 2026-08-08 12:00:08 | 0 | ||||||
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Wake Forest University Pharmacology Resource Report Resource Website |
Wake Forest University Pharmacology (RRID:SCR_013111) | postdoctoral program resource, data or information resource, graduate program resource, training resource, people resource, portal, organization portal | The pursuit of the Department of Physiology & Pharmacology at Wake Forest University School of Medicine is excellence in research and education. Graduate education and training includes quality introductory and advanced courses in physiology, pharmacology and neuroscience, as well as seminars and journal clubs in several major research areas. Laboratory rotations encourage the graduate student to explore various experimental approaches and provide a diverse training experience. The department and Medical Center are frequented by distinguished visitors from other universities who further enrich the stimulating academic environment. Departmental faculty are active in the medical education as well as in residency training programs in Neurology, Psychiatry, Urology, and Surgery. | nif-0000-02297 | SCR_013111 | Wake Forest U | 2026-08-08 12:00:19 | 0 | |||||||||||
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LifeScope Resource Report Resource Website 100+ mentions |
LifeScope (RRID:SCR_013234) | LifeScope | software resource | Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC). | unix/linux, life technologies, linux, next-generation sequencing | has parent organization: Life Technologies | Acknowledgement requested | OMICS_00667 | SCR_013234 | LifeScope Genomic Analysis Software | 2026-08-08 12:00:09 | 200 | |||||||
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CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | 2026-08-08 12:00:20 | 1 | ||||||||||
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CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-08-08 12:00:08 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-08-08 11:59:53 | 68 | ||||||||||
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HMMSplicer Resource Report Resource Website 1+ mentions |
HMMSplicer (RRID:SCR_013315) | HMMSplicer | software resource | An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
OMICS_01241 | SCR_013315 | 2026-08-08 11:59:55 | 4 | ||||||||||
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Lab Vision Resource Report Resource Website 1+ mentions |
Lab Vision (RRID:SCR_013436) | commercial organization, antibody supplier, reagent supplier, material resource | An Antibody supplier | nlx_152395 | SCR_013436 | 2026-08-08 12:00:22 | 4 | ||||||||||||
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Sequencing of Candida Albicans Resource Report Resource Website 10+ mentions |
Sequencing of Candida Albicans (RRID:SCR_013437) | data or information resource, portal, topical portal | The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects. | stanford, genome, technology, shotgun, sequencing, strain, haploid, gene, nucleation, health, life, aids, drug, patient | has parent organization: Stanford University; Stanford; California | Burroughs Wellcome Fund ; NIDCR DE12302-02S2; NIAID RO1AI16567; NIAID RO1AI46351; NIAID NO1AI05406; NIDCR R01DE12940; NIDCR P01DE07946 |
nif-0000-30294 | SCR_013437 | Candida Albicans | 2026-08-08 11:59:56 | 21 | ||||||||
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Molecular Probes Resource Report Resource Website 10000+ mentions |
Molecular Probes (RRID:SCR_013318) | commercial organization, antibody supplier, reagent supplier, material resource | An Antibody supplier and subset of ThermoFisher Scientific which provides fluorescence reagents for various experiments and methods. | antibody supplier, fluorescence reagent | is affiliated with: Thermo Fisher Scientific | Pay per product | nlx_152414 | http://www.invitrogen.com/ | SCR_013318 | Invitrogen, Molecular Probes (Invitrogen) | 2026-08-08 12:00:21 | 16872 | |||||||
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Montage RTS2000 Resource Report Resource Website |
Montage RTS2000 (RRID:SCR_013439) | image processing software, software resource, software application, data processing software | Software program for creating montages from multiphoton microscopy. | microscopy, mosaic, montage, image |
is listed by: 3DVC has parent organization: National Center for Microscopy and Imaging Research |
NCRR P41 RR04050 | GNU General Public License | nif-0000-10515 | SCR_013439 | 2026-08-08 12:00:11 | 0 | ||||||||
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L2L Microarray Analysis Tool Resource Report Resource Website 1+ mentions |
L2L Microarray Analysis Tool (RRID:SCR_013440) | L2L | data or information resource, production service resource, software resource, data analysis service, software application, database, analysis service resource, service resource, data analysis software, storage service resource, data repository, data processing software |
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019. Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible |
microarray, gene expression, adipogenesis, biological, biological process, cancer, cell cycle regulator, cellular component, chromatin, cockayne syndrome, dna damage, growth factor, hormone, human biology, hypoxic response, immune mediator, inflammatory mediator, molecular function, molecular neuroanatomy resource, adipocyte, development, hypoxia, immune, inflammation, metabolism, mitogen, neuro, rna, vascular, transcription, tissue, splicing, mouse, human, rat, source code, statistical analysis, gene, chromatin structure |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Washington; Seattle; USA |
Cockayne syndrome, DNA damage, Other, Aging, Cancer | Cora May Poncin Foundation ; NIGMS GM41624 |
PMID:16168088 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10463 | http://depts.washington.edu/l2l/about.html | SCR_013440 | L2L Microarray Database, L2L Microarray Analysis Tool: A simple tool for discovering the hidden biological significance in microarray expression data, L2L MDB | 2026-08-08 12:00:22 | 1 | |||
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Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | 2026-08-08 12:00:10 | 72 | ||||||||
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Kokusan Chemical Resource Report Resource Website |
Kokusan Chemical (RRID:SCR_013443) | commercial organization, antibody supplier, reagent supplier, material resource | An Antibody supplier | nlx_152394 | SCR_013443 | Kokusan Chemical Co. Ltd. | 2026-08-08 11:59:56 | 0 | |||||||||||
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NEUMA Resource Report Resource Website 1+ mentions |
NEUMA (RRID:SCR_013324) | NEUMA | software resource | Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. |
is listed by: OMICtools has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
PMID:21059678 | OMICS_01281 | SCR_013324 | Normalization by Expected Uniquely Mappable Area | 2026-08-08 12:00:21 | 5 | ||||||||
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ZFIN Antibody Wiki Resource Report Resource Website |
ZFIN Antibody Wiki (RRID:SCR_013326) | wiki, data or information resource, narrative resource | A catalog of antibodies important for zebrafish research, maintained by ZFIN. ZFIN Antibody Wiki is where zebrafish researchers can help each other by sharing antibody information - new antibodies, protocols, tips - anything that might be helpful. | has parent organization: Zebrafish Information Network (ZFIN) | nlx_38706 | SCR_013326 | ZFIN Community Antibody Wiki | 2026-08-08 11:59:55 | 0 | ||||||||||
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chimerascan Resource Report Resource Website 50+ mentions |
chimerascan (RRID:SCR_013298) | chimerascan | software resource | Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data. | Gene fusion detection, paired-end RNA sequencing data, RNA sequencing data, chimeric transcripts detection, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:chimerascan, OMICS_01343 | https://bio.tools/chimerascan | SCR_013298 | 2026-08-08 12:00:21 | 53 | |||||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | data or information resource, production service resource, web service, software resource, data analysis service, data access protocol, database, analysis service resource, service resource, storage service resource, data repository | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-08-08 11:59:55 | 1324 | ||||||
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Center for New Technology Enterprise Resource Report Resource Website |
Center for New Technology Enterprise (RRID:SCR_013333) | CNTE | data or information resource, portal, training resource, topical portal | It is an independent nonprofit organization established to provide meaningful trans-disciplinary experiential education to students by making the most cutting-edge instructional methods and technologies available to them to bring new inventions to the marketplace and to encourage knowledge sharing and collaboration among its numerous constituencies. The Center provides a comprehensive program in which its students learn and acquire real-world experience by assisting universities, private and public research institutions, companies, and entrepreneurs to evaluate new technologies and facilitate the creation and development of new ventures. By offering a virtual venue for students and other constituencies worldwide, our stakeholders and collaborators can connect and share knowledge, expertise, resources, best practices, and other important information. Employers, investors and others searching for talent place a premium on relevant experience. However, students, individuals seeking a change in their careers, and prospective entrepreneurs often find it difficult to obtain positions that can provide needed experience, even if they are willing to work without compensation. This conundrum often leads to people taking or staying in positions for which they have no passion and which do not make the best use of their abilities. The Centers program is designed to provide extensive, intensive and relevant experience to its participants, with particular emphasis on teaching them to adapt to and thrive in our lightning fast, rapidly changing and increasingly flat world. As an independent organization, the Centers program and activities are not restricted to any particular institution or jurisdiction. Thus the Center can attract students, clients, professionals and other stakeholders, establish collaborations, and pursue other opportunities appropriate to its mission almost anywhere. eductional resource. | nif-0000-00461 | SCR_013333 | The Center for New Technology Enterprise, Center for New Technology Enterprise | 2026-08-08 12:00:21 | 0 | ||||||||||
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Probalign Resource Report Resource Website 10+ mentions |
Probalign (RRID:SCR_013332) | Probalign | image analysis software, software resource, software application, alignment software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats. |
is used by: eProbalign is listed by: OMICtools is listed by: Debian has parent organization: New Jersey Institute of Technology; New Jersey; USA |
PMID:16954142 DOI:10.1093/bioinformatics/btl472 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00985 | https://sources.debian.org/src/probalign/ | SCR_013332 | Probalign: multiple sequence alignment using partition function posterior probabilities | 2026-08-08 12:00:10 | 16 |
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