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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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FisWidgets Resource Report Resource Website |
FisWidgets (RRID:SCR_007367) | data analysis software, data processing software, software application, software resource | A set of Java libraries for rapidly creating GUIs for software modules (C, C++, Fortan, PERL scripts, etc.), and graphically controlling process flow among them. This allows a GUI to be created for existing image processing and analysis routines, which provides: 1) graphic elements for setting parameters, arguments, etc. (i.e., text dialogs, file browsers, etc.); 2) links to web based documentation; 3) simple point-and-click interface for setting up a path for data flow from one module to another. The purpose of FisWidgets is to provide an integrated and user-friendly environment for using the disparate and growing array of image processing and analysis tools created by different laboratories. | has parent organization: University of Pittsburgh; Pennsylvania; USA | nif-0000-00302 | http://neurocog.lrdc.pitt.edu/fiswidgets/ | SCR_007367 | SciCrunch Registry | 2026-10-31 12:14:41 | 0 | ||||||||||
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CardioGenomics Resource Report Resource Website 1+ mentions |
CardioGenomics (RRID:SCR_007248) | CardioGenomics | data or information resource, portal, topical portal | The primary goal of the CardioGenomics PGA is to begin to link genes to structure, function, dysfunction and structural abnormalities of the cardiovascular system caused by clinically relevant genetic and environmental stimuli. The principal biological theme to be pursued is how the transcriptional network of the cardiovascular system responds to genetic and environmental stresses to maintain normal function and structure, and how this network is altered in disease. This PGA will generate a high quality, comprehensive data set for the functional genomics of structural and functional adaptation of the cardiovascular system by integrating expression data from animal models and human tissue samples, mutation screening of candidate genes in patients, and DNA polymorphisms in a well characterized general population. Such a data set will serve as a benchmark for future basic, clinical, and pharmacogenomic studies. Training and education are also a key focus of the CardioGenomics PGA. In addition to ongoing journal clubs and seminars, the PGA will be sponsoring symposia at major conferences, and developing workshops related to the areas of focus of this PGA. Information regarding upcoming events can be found in the Events section of this site, and information about training and education opportunities sponsored by CardioGenomics can be found on the Teaching and Education page. The CardioGenomics project came to a close in 2005. This server, cardiogenomics.med.harvard.edu, remains online in order to continue to distribute data that was generated by investigators under the auspices of the CardioGenomics Program for Genomic Applications (PGA). :Sponsors: This resource is supported by The National Heart, Lung and Blood Institute (NHLBI) of the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomics, clinical, genetic, environmental, stimulus, cardiovascular, disease, data, expression, gene, dna, polymorphism, population, pharmacogenomic, training, education | has parent organization: Harvard University; Cambridge; United States | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30296 | http://www.cardiogenomics.org | SCR_007248 | SciCrunch Registry | The CardioGenomics Project | 2026-10-31 12:14:43 | 6 | ||||||
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Image Pro Plus Resource Report Resource Website 10000+ mentions |
Image Pro Plus (RRID:SCR_007369) | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data. | morphometric, image analysis, image acquisition, automation, classification, microscope control | is listed by: SoftCite | nif-0000-00313, SCR_015803, SCR_016879 | SCR_007369 | SciCrunch Registry | Image-Pro Plus, Image-Pro Plus Morphometric Analysis Software | 2026-10-31 12:14:36 | 18774 | |||||||||
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British Neuroscience Association Resource Report Resource Website |
British Neuroscience Association (RRID:SCR_007402) | institution | The British Neuroscience Association, formerly known as The Brain Research Association, was officially relaunched in 1997, continuing many of the traditions of the BRA but with a professional and revamped style. Membership has increased dramatically since this time, now standing at 2000, and the BNA has increasingly taken a leading role in major events, such as hosting the Second Forum of European Neuroscience in Brighton in June, 2000. The BNA is the largest body representing all aspects of neuroscience from ion channels to whole animal behaviour. The Aims and Objectives of the Association are as follows: 1. To promote on a multidisciplinary basis the study of the development structure and function of the nervous system in health and disease. 2. To promote the dissemination of information to all those interested in the neurosciences and related disciplines by means of lectures, discussions, meetings and reports from time to time obtained from such researchers. 3. To advise as far as possible on issues in neurosciences related to health and disease. 4. To endeavour to increase public awareness and understanding of neuroscience research in health and disease. 5. To assist in the training of neuroscientists and other professionals engaged in neuroscience teaching and research. The BNA achieves these aims as follows: 1. By hosting a national meeting biennially, by publishing the proceedings of that meeting and distributing them to the scientific community. 2. By organising a number of focussed ''One Day symposia'' during the year, contributing to training courses for young neuroscientists and organising public lectures and events . 3. By regularly distributing information by the BNA Newsletter or by the BNA News E-mail Alert facility that can inform members about other relevant events, publications and topical issues. 4. By encouraging attendance at its own national meeting and those to which it is affiliated by awarding bursaries to students and young postdoctoral workers, and facilitating participation in the Society for Neuroscience annual meeting by offering sponsored abstract forms. 5. By awarding graduate and undergraduate prizes, and special awards to senior neuroscientists and to lay people who have contributed significantly through their own charitable work to the success of our discipline. 6. By constantly negotiating special discount prices of relevant books and journals, and by offering free online access to the European Journal of Neuroscience.The BNA is the fastest growing learned society, now boasting more than 2000 members, a rise of more than 40% since its relaunch as the BNA in 1997 from the former Brain Research Association. In addition to discounted journals and books and other occasional ''special offers'', the benefits of membership now include the following: 1. Reduced registration fees (up to 50%) to the National Meeting, and FREE admission to many events throughout the year including ''One Day Symposia'' and The Christmas Symposium. 2. Regular mailing of BNA Bulletin and other relevant items. 3. Regular BNA and FENs Email Alert service. 4. Student prizes, and bursaries for attendance at BNA, FENS and IBRO meetings. 5. Free on-line access to European Journal of Neuroscience. 6. Concessionary (SFN membership rate) registration fees and sponsored abstract forms for Society for Neuroscience annual meeting. 7. Free advertising in the BNA Bulletin and on the BNA Website. 8. Free (automatic) membership of the Federation of European Neuroscience Societies (FENS), the International Brain Research Organisation (IBRO) and the Biosciences Federation (BSF). educational resource; jobs. | ISNI: 0000 0000 9361 5178, nif-0000-00460, grid.507170.4, Wikidata: Q4970552 | https://ror.org/05sfhjs05 | SCR_007402 | SciCrunch Registry | BNA | 2026-10-31 12:14:37 | 0 | ||||||||||
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Autism Society of America Resource Report Resource Website 1+ mentions |
Autism Society of America (RRID:SCR_007401) | ASA | nonprofit organization | ASA, the nations leading grassroots autism organization, exists to improve the lives of all affected by autism. We do this by increasing public awareness about the day-to-day issues faced by people on the spectrum, advocating for appropriate services for individuals across the lifespan, and providing the latest information regarding treatment, education, research and advocacy. :Founded in 1965 by Dr. Bernard Rimland, Dr. Ruth Sullivan and many other parents of children with autism, ASA is the leading source of trusted and reliable information about autism. Through its strong chapter network, ASA has spearheaded numerous pieces of state and local legislation, including the 2006 Combating Autism Act, the first federal autism-specific law. ASAs website is one of the most visited websites on autism in the world and its quarterly journal, Autism Advocate, has a broad national readership. ASA also hosts the most comprehensive national conference on autism, attended by 2000 people each year. Our information and referral team, our program staff, and our strong chapter presence serve thousands of families each year who are searching for help in their journey with autism. :ASAs national office is headquartered in Bethesda, Maryland. ASA is a member and chapter organization whos national Board of Directors is composed of democratically elected members and appointed members. We are proud to be one of the few organizations to have members with autism serving as active board directors. ASAs Panel of Professional Advisors sets the standards for our Options Policy that governs our practices, and we are proud to count the top professional experts in autism on our PPA. ASAs Panel of People on the Spectrum of Autism Advisors is a first-of-its-kind advisory panel comprised solely of individuals with autism, who help ASA staff create programs and services that will advocate for the rights of all people with autism to live fulfilling, interdependent lives. :Each year, people with autism, families and professionals volunteer thousands of hours to help ASA achieve its mission of serving all those affected by autism. To each and every one of you, thank you : | ISNI: 0000 0000 8941 9107, nif-0000-00459, grid.432021.6, Crossref funder ID: 100003613 | https://ror.org/05hzvxx71 | SCR_007401 | SciCrunch Registry | ASA | 2026-10-31 12:14:41 | 2 | |||||||||
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COLELMS: Stata module to calculate Coles LMS values for growth data Resource Report Resource Website 1+ mentions |
COLELMS: Stata module to calculate Coles LMS values for growth data (RRID:SCR_007244) | data analysis software, data processing software, software application, software resource | COLELMS calculates LMS values, smoothed LMS, and growth reference centiles based in smoothed LMS values. df value is set to when calculating smoothed LMS values. You are responsible for setting an appropriate df for your data. This is version 0.2 of the software. Sponsors: This resource is supported by Boston College. Keywords: Software, LMS, Calculation, Growth, Data, Stata, Module, | nif-0000-30264 | SCR_007244 | SciCrunch Registry | COLELMS | 2026-10-31 12:14:40 | 7 | |||||||||||
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XFido Resource Report Resource Website |
XFido (RRID:SCR_007365) | data processing software, data visualization software, software application, software resource | An interactive, graphic, fiducial marking software for placing, editing and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view the tilt series as well as crop it. | has parent organization: National Center for Microscopy and Imaging Research | nif-0000-00300 | SCR_007365 | SciCrunch Registry | XFido | 2026-10-31 12:14:44 | 0 | ||||||||||
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Hiclib Resource Report Resource Website 10+ mentions |
Hiclib (RRID:SCR_005535) | Hiclib | software resource | An Software resource | is listed by: OMICtools | OMICS_00521 | SCR_005535 | SciCrunch Registry | 2026-10-31 12:14:17 | 22 | ||||||||||
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SHRiMP Resource Report Resource Website 100+ mentions |
SHRiMP (RRID:SCR_005496) | SHRiMP | software resource | A software package for aligning genomic reads against a target genome. | next generation sequencing, alignment |
is used by: Jambalaya is listed by: OMICtools is related to: Jambalaya is related to: Proovread has parent organization: University of Toronto; Ontario; Canada |
PMID:21278192 | OMICS_00685 | SCR_005496 | SciCrunch Registry | SHRiMP - SHort Read Mapping Package | 2026-10-31 12:14:13 | 208 | |||||||
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BrainEthics Resource Report Resource Website |
BrainEthics (RRID:SCR_005530) | BrainEthics | blog, book, data or information resource, narrative resource | There are a lot of fine blogs out there covering the avalance of current neuroscience research. With this blog Thomas Rams��y & Martin Skov want to highlight the many consequences of this growing understanding of the human brain. We are especially interested in two types of consequences: Tinkering with the brain and What is it like to be a human being? * Tinkering with the brain: First and foremost, with an understanding of how the brain works comes the possibility of tinkering with it. We already use billions of dollars every year on psychopharmocologia trying to treat depression, schizophrenia, obsessive-compulsive disorder and other mental diseases. But should we also use our knowledge of the brain to treat undesirable mental traits such as pedophilia or sociopathy? And what about enhancing normal brains? Clearly, evolution hasn''t endowed us with the most efficient brain imaginable. Shouldn''t we do something about its many shortcomings? * What is it like to be a human being?: Secondly, our view of human behavior is sure to change with our improved understanding of the human brain. Our knowledge of core human faculties such as language, social reasoning, aesthetics, and economics is already being challenged by modern neuroscience, yielding multiple hard questions. Do we have a free will? Is the mind innate or plastic? If people are not responsible for their actions (since all actions are caused by blind molecular processes) does our legal system still make sense? In short, will modern neuroscience come to completely redefine human nature? We try to discuss contemporary research literature, not just news reports. Although we will occasionally also target popular science reports, since we believe they play an important role in dissemining lessons from the lab. And in the future we plan to also post interviews with interesting researchers, as well as link to our own publications in journals and books. Additionally, the latest and most important books in the multidisciplinary field of neuroscience, cognition, psychology, ethics and economics are presented. | brain, science, ethics, neuroethics, human, behavior | is parent organization of: BrainEthics Podcast | nlx_144626 | SCR_005530 | SciCrunch Registry | Brain Ethics, BrainEthics - Consequences of Brain Science | 2026-10-31 12:14:17 | 0 | ||||||||
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SMALT Resource Report Resource Website 500+ mentions |
SMALT (RRID:SCR_005498) | SMALT | software resource | Software that aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads. |
is listed by: OMICtools is related to: Sequence Search and Alignment by Hashing Algorithm has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00686 | SCR_005498 | SciCrunch Registry | 2026-10-31 12:14:07 | 516 | ||||||||||
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French Ministry of Higher Education and Research Resource Report Resource Website 10+ mentions |
French Ministry of Higher Education and Research (RRID:SCR_005532) | MESR | institution | Ministry of Higher Education, Research and Innovation, France is one of the 900 Higher Education-related Organizations and Associations. |
is parent organization of: CIRAD is parent organization of: French National Center for Scientific Research |
ISNI: 0000 0001 2369 5464, Wikidata: Q2726949, grid.425729.f, Crossref funder ID: 501100004792, nlx_143604 | https://ror.org/03sjk9a61 | SCR_005532 | SciCrunch Registry | Ministere de i''Enseignement Supereur et de la Recherche, Ministere de l''Enseignement Supérieur et de la Recherche, French Ministry of Research, The Ministry, Le ministre | 2026-10-31 12:14:15 | 38 | ||||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, data set, database | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | SciCrunch Registry | TIGRFAMs | 2026-10-31 12:14:14 | 142 | ||||
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Segemehl Resource Report Resource Website 10+ mentions |
Segemehl (RRID:SCR_005494) | Segemehl | software resource | A software to map short sequencer reads to reference genomes. It is able to detect not only mismatches but also insertions and deletions. Furthermore, it is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Leipzig; Saxony; Germany |
PMID:24512684 PMID:22581174 PMID:19750212 DOI:10.1371/journal.pcbi.1000502 |
Acknowledgement requested, Free, Public | biotools:segemehl, OMICS_00683 | https://bio.tools/segemehl, https://sources.debian.org/src/segemehl/ | SCR_005494 | SciCrunch Registry | segemehl - short read mapping with gaps | 2026-10-31 12:14:07 | 48 | |||||
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PASS Resource Report Resource Website 1000+ mentions |
PASS (RRID:SCR_005490) | PASS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: PASS-bis has parent organization: University of Padua; Padua; Italy |
PMID:19218350 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pass, OMICS_00673 | https://bio.tools/pass | SCR_005490 | SciCrunch Registry | PASS: a program to align short sequences | 2026-10-31 12:14:16 | 2085 | |||||
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Ministry of Health; Rome; Italy Resource Report Resource Website 100+ mentions |
Ministry of Health; Rome; Italy (RRID:SCR_005526) | institution | Governmental agency of Italy. Its headquarters are in Rome and is led by the Italian Minister of Health. | Government granting agency | nlx_158316, Crossref funder ID: 501100003196, grid.415788.7, Wikidata: Q745634, ISNI: 0000 0004 1756 9674 | https://ror.org/00789fa95 | SCR_005526 | SciCrunch Registry | Italian Ministry of Health, Ministry of Health, Ministero della Salute | 2026-10-31 12:14:08 | 131 | |||||||||
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Fulcrum Resource Report Resource Website 1+ mentions |
Fulcrum (RRID:SCR_005523) | Fulcrum | software resource | Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory. | illumina, 454, read, paired-end read, single-end read, high-throughput sequencing, redundant read, genome, transcriptome, ultra high throughput sequencing |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22419786 | BSD-like license | OMICS_01049 | http://pringlelab.stanford.edu/protocols.html | SCR_005523 | SciCrunch Registry | Fulcrum Read Collapser | 2026-10-31 12:14:17 | 4 | |||||
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Randox Life Sciences Resource Report Resource Website 1+ mentions |
Randox Life Sciences (RRID:SCR_005525) | commercial organization | An Antibody supplier | nlx_152446 | SCR_005525 | SciCrunch Registry | Randox Laboratories Ltd. | 2026-10-31 12:14:15 | 7 | |||||||||||
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Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | OMICS_00668, biotools:maq | https://bio.tools/maq, https://sources.debian.org/src/maq/ | SCR_005485 | SciCrunch Registry | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-10-31 12:14:06 | 74 | |||||
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MOSAIK Resource Report Resource Website 50+ mentions |
MOSAIK (RRID:SCR_005486) | MOSAIK | software resource | A reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into Mosaik?s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs. At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format. Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, FreeBSD, and Linux operating systems. Other platforms can easily be supported upon request. MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor. MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope. | next-generation sequencing, alignment, smith-waterman algorithm, c++, computational biology, reference guided aligner |
is listed by: OMICtools is listed by: Debian is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Google Code |
Free, Freely available | OMICS_00669 | https://sources.debian.org/src/mosaik-aligner/ | SCR_005486 | SciCrunch Registry | mosaik-aligner | 2026-10-31 12:14:16 | 87 |
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