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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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San Diego Supercomputer Center Resource Report Resource Website 1+ mentions |
San Diego Supercomputer Center (RRID:SCR_001856) | SDSC | institution | Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing. SDSC is considered a leader in data-intensive computing, providing resources, services and expertise to the national research community including industry and academia. The mission of SDSC is to extend the reach of scientific accomplishments by providing tools such as high-performance hardware technologies, integrative software technologies, and deep interdisciplinary expertise to these communities. From 1997 to 2004, SDSC extended its leadership in computational science and engineering to form the National Partnership for Advanced Computational Infrastructure (NPACI), teaming with approximately 40 university partners around the country. Today, SDSC is an Organized Research Unit of the University of California, San Diego with a staff of talented scientists, software developers, and support personnel. A broad community of scientists, engineers, students, commercial partners, museums, and other facilities work with SDSC to develop cyberinfrastructure-enabled applications to help manage their extreme data needs. Projects run the gamut from creating astrophysics visualization for the American Museum of Natural History, to supporting more than 20,000 users per day to the Protein Data Bank, to performing large-scale, award-winning simulations of the origin of the universe or how a major earthquake would affect densely populated areas such as southern California. Along with these data cyberinfrastructure tools, SDSC also offers users full-time support including code optimization, training, 24-hour help desk services, portal development and a variety of other services. As one of the NSF's first national supercomputer centers, SDSC served as the data-intensive site lead in the agency's TeraGrid program, a multiyear effort to build and deploy the world's first large-scale infrastructure for open scientific research. SDSC currently provides advanced user support and expertise for XSEDE (Extreme Science and Engineering Discovery Environment) the five-year NSF-funded program that succeeded TeraGrid in mid-2011. | engineering, bioinformatics, computing, geoinformatics, hardware, industry, science, software, technology, computational science, supercomputing, cyberinfrastructure |
has parent organization: University of California at San Diego; California; USA is parent organization of: Scaffold builder is parent organization of: OpenTopography is parent organization of: chronopolis is parent organization of: XSEDE - Extreme Science and Engineering Discovery Environment is parent organization of: Family Pairwise Search - Protein Family Classification is parent organization of: Neuroscience Gateway is parent organization of: Magnetics Information Consortium |
NSF | Free, Freely available | nif-0000-10418, Wikidata: Q3947008, grid.419957.7 | https://ror.org/04mg3nk07 | SCR_001856 | 2026-02-14 02:00:09 | 5 | ||||||
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National Society of Genetic Counselors Resource Report Resource Website 10+ mentions |
National Society of Genetic Counselors (RRID:SCR_001803) | NSGC | institution | Professional society of genetic counselors that promotes networking, continuing education opportunities, advocacy, and discussion of relevant issues in the field of genetics. | genetics, counselor, advocacy, professional society, professional network | Free | Crossref funder ID: 100010237, grid.429579.4, nif-0000-10367, ISNI: 0000 0001 2179 5189 | https://ror.org/02ja4sy98 | SCR_001803 | National Society of Genetic Counselors (NSGC) | 2026-02-14 02:00:08 | 16 | |||||||
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RchyOptimyx Resource Report Resource Website 1+ mentions |
RchyOptimyx (RRID:SCR_001889) | software resource | Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response). | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23044634 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05637 | SCR_001889 | RchyOptimyx - Optimyzed Cellular Hierarchies for Flow Cytometry, RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry | 2026-02-14 02:00:14 | 3 | |||||||
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CQN Resource Report Resource Website 1+ mentions |
CQN (RRID:SCR_001786) | CQN | software resource | A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. | rna-seq, differential expression, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:22285995 | Free, Available for download, Freely available | OMICS_01949, biotools:cqn | https://bio.tools/cqn | SCR_001786 | Conditional Quantile Normalization | 2026-02-14 02:00:11 | 6 | |||||
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PoissonSeq Resource Report Resource Website 10+ mentions |
PoissonSeq (RRID:SCR_001784) | PoissonSeq | software resource | Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data. | normalization, testing, false discovery rate, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
PMID:22003245 | Free, Available for download, Freely available | OMICS_01950 | http://cran.r-project.org/web/packages/PoissonSeq/index.html | SCR_001784 | PoissonSeq: Significance analysis of sequencing data based on a Poisson log linear model | 2026-02-14 02:00:11 | 33 | |||||
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SNPper Resource Report Resource Website 10+ mentions |
SNPper (RRID:SCR_001963) | SNPper | software resource | Retrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions. | single-nucleotide polymorphism, gene, chromosome |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:12490454 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01926 | SCR_001963 | 2026-02-14 02:00:21 | 49 | |||||||
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National Center for PTSD Resource Report Resource Website 10+ mentions |
National Center for PTSD (RRID:SCR_001967) | NCPTSD | institution | We are the center of excellence for research and education on the prevention, understanding, and treatment of PTSD. Our Center has seven divisions across the country. Although we provide no direct clinical care, our purpose is to improve the well-being and understanding of American Veterans. We conduct cutting edge research and apply resultant findings to: Advance the Science and Promote Understanding of Traumatic Stress. The National Center has emerged as the world's leading research and educational center of excellence on PTSD. Its vision is to be the foremost leader in information on PTSD and trauma; information generated internally through its extensive research program, and information synthesized from published scientific research and collective clinical experience that is efficiently disseminated to the field. The Center is organized to facilitate rapid translation of science into practice, assuring that the latest research findings inform clinical care; and translation of practice into science, assuring that questions raised by clinical challenges are addressed using rigorous experimental protocols. By drawing on the specific expertise vested at each separate division (e.g., behavioral, neuroscientific, etc.), the National Center provides a unique infrastructure within which to implement multidisciplinary initiatives regarding the etiology, pathophysiology, diagnosis and treatment of PTSD. | post-traumatic stress disorder, stress, trauma, treatment, stress-related disorder, clinical care, human, traumatic stress disorder, one mind ptsd | has parent organization: U.S. Department of Veterans Affairs | US Department of Veterans Affairs | nif-0000-10538, grid.497281.1, ISNI: 0000 0004 0374 606X | https://ror.org/01dbbht76 | http://www.ncptsd.va.gov/ | SCR_001967 | National Center for Posttraumatic Stress Disorder, VA National Center for PTSD | 2026-02-14 02:00:12 | 11 | |||||
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Parkinson Society Canada Resource Report Resource Website 1+ mentions |
Parkinson Society Canada (RRID:SCR_002014) | nonprofit organization | A not-for-profit, volunteer based charity whose purpose is to find a cure for Parkinson's disease through research, advocacy, education and support services. Parkinson Society Canadas leads initiatives that include: raising funds for research through national events; funding research, movement disorder clinics, and outreach programs across Canada; staffing a national Information and Referral Centre; developing educational and information materials; providing up to date detailed information about Parkinson's disease; and providing support for regional partners to better meet the needs of people living with Parkinson's services. Researchers can apply for various funding awards and fellowships by following the funding process outlined by Parkinson Society Canada. | parkinson's disease, parkinson's disease online community, parkinson's disease organizations, parkinson's disease patient care, parkinson's disease therapy, parkinson's disease treatment center | Parkinson's Disease | Public, Funding is available to researchers in the form of awards and fellowships | grid.453461.1, Crossref funder ID: 501100000263, nif-0000-11672 | https://ror.org/04amfk357 | SCR_002014 | 2026-02-14 02:00:13 | 3 | ||||||||
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Model 1025 MR-compatible Small Animal Monitoring and Gating System Resource Report Resource Website 1+ mentions |
Model 1025 MR-compatible Small Animal Monitoring and Gating System (RRID:SCR_002090) | Model 1025 Monitoring & Gating System | instrument resource | Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2. | hardware, instrument, equipment, physiology, monitoring, gating, mr environment, respiration, temperature, blood pressure, oxygen saturation, end-tidal co2, magnetic resonance, electrocardiogram, magnetic resonance imaging, software resource | Free, Freely available | SciRes_000157 | https://wikihost.uib.no/mriwiki/images/4/4c/SAInstruments_1025.pdf | http://www.i4sa.com/web_app/main/defaultProduct.aspx?ID=82&PT=3 | SCR_002090 | Model 1025 Monitoring and Gating System, MR-Compatible Model 1025 Monitoring and Gating System, Small Animal Monitoring and Gating System | 2026-02-14 02:00:22 | 3 | ||||||
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Korea National Institute of Health Resource Report Resource Website 10+ mentions |
Korea National Institute of Health (RRID:SCR_001959) | KNIH | institution | Institute dedicated to medical research to improve biomedical innovation and public health in South Korea. | health research institute, south korea | is parent organization of: Genovar | THIS RESOURCE IS NO LONGER IN SERVICE | grid.415482.e, nlx_156100, ISNI: 0000 0004 0647 4899, Crossref funder ID: 501100003653 | https://ror.org/00qdsfq65 | SCR_001959 | Korea NIH | 2026-02-14 02:00:15 | 11 | ||||||
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flowType Resource Report Resource Website 1+ mentions |
flowType (RRID:SCR_001957) | software resource | Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22383736 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05613 | SCR_001957 | flowType - Phenotyping Flow Cytometry Assays | 2026-02-14 02:00:15 | 9 | |||||||
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Minimum Information for Biological and Biomedical Investigations Resource Report Resource Website 1+ mentions |
Minimum Information for Biological and Biomedical Investigations (RRID:SCR_002042) | MIBBI | data or information resource, narrative resource, standard specification | A common portal for minimum information (MI) checklists to act as a one-stop shop for those exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration. Goals include * To increase the visibility of projects developing guidance for the reporting of biological and biomedical science. * To encourage appropriate collaborative development between projects to avoid duplication of effort or competition. * To promote the adoption of consensus guidance on reporting by journals and funders. | minimum information, bioscience, metadata standard, MDAR |
lists: MIAPA lists: Minimum Information About a Simulation Experiment is listed by: FORCE11 is related to: Genomic Standards Consortium is related to: MIGen has parent organization: FAIRsharing |
BBSRC BB/E025080/1 | PMID:18688244 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-12075 | http://www.mibbi.org/ http://mibbi.sourceforge.net/ https://www.force11.org/node/4660 |
http://www.biosharing.org/mibbi | SCR_002042 | MIBBI: Minimum Information for Biological and Biomedical Investigations | 2026-02-14 02:00:17 | 1 | |||
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Brain and Behavior Research Foundation Resource Report Resource Website 10+ mentions |
Brain and Behavior Research Foundation (RRID:SCR_001992) | data or information resource, funding resource, portal, topical portal |
The Brain and Behavior Research Foundation (formerly NARSAD, the National Alliance for Research on Schizophrenia and Depression) is committed to alleviating the suffering of mental illness by awarding grants that will lead to advances and breakthroughs in scientific research. Additionally, learn about brain and behavior disorders and upcoming events. 100% of all donor contributions for research are invested in NARSAD Grants leading to discoveries in understanding causes and improving treatments of disorders in children and adults, such as depression, bipolar disorder, schizophrenia, autism, attention deficit hyperactivity disorder, and anxiety disorders like obsessive-compulsive and post-traumatic stress disorders. Over a quarter of a century, we have awarded nearly $300 million worldwide to more than 3,000 scientists carefully selected by our prestigious Scientific Council. We receive no government funding. All of our work relies on contributions from families, foundations and other caring donors. |
adult, child, attention deficit-hyperactivity disorder, autism, behavior disorder, bipolar disorder, brain, depressive disorder, human, mental health, research, mental disease, neuropsychiatric illness, proceedings, grant, schizophrenia, post-traumatic stress disorder, anxiety disorder, autism, obsessive-compulsive disorder | nif-0000-12459 | http://www.narsad.org/ | SCR_001992 | National Alliance on Research in Schizophrenia and Depression, NARSAD: The Worlds Leading Charity Dedicated to Mental Health Research, NARSAD: The Brain and Behavior Research Fund, Brain & Behavior Research Foundation, Brain Behavior Research Foundation, National Alliance for Research on Schizophrenia Depression | 2026-02-14 02:00:16 | 26 | |||||||||
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International Society for Magnetic Resonance in Medicine Resource Report Resource Website 1+ mentions |
International Society for Magnetic Resonance in Medicine (RRID:SCR_001988) | ISMRM | institution | The International Society for Magnetic Resonance in Medicine is an international, nonprofit, scientific association whose purpose is to promote communication, research, development, and applications in the field of magnetic resonance in medicine and biology and other related topics and to develop and provide channels and facilities for continuing education in the field. In addition to its large scientific meetings, the Society holds workshops and publishes two journals, Magnetic Resonance in Medicine and the Journal of Magnetic Resonance Imaging, and a newsletter, MR Pulse. It also sponsors study groups on specific areas of scientific interest and chapters based on geographical location. Its multidisciplinary membership of over 6,000 consists of clinicians, physicists, engineers, biochemists, and technologists. The ISMRMs inception, on January 1, 1994, resulted from a merger of the Society of Magnetic Resonance in Medicine and the Society of Magnetic Resonance Imaging forming the Society of Magnetic Resonance (now named the International Society for Magnetic Resonance in Medicine). The purposes of the Society are: (A) (i) To promote communication, research, development, applications, and the availability of information on magnetic resonance in medicine and biology and other related topics internationally; (ii) To develop and provide channels and facilities for continuing education and communication in the field, to publish and assist in the publishing of journals and other publications in the field; and (iii) To provide information and advice on those aspects of public policy which are concerned with magnetic resonance in medicine and biology and other related topics, and otherwise perform charitable, scientific and educational functions with respect to magnetic resonance applications in medicine and biology and other related topics. (B) To work with or for, and to co-operate with local, regional and national governments and governmental and private agencies, organizations, firms and institutions in efforts to accomplish one or more of the above purposes. (C) To ensure that scientists and clinicians working in the field have equal and fair opportunities to contribute to it. The site lists a partial list of NMR and MRI resources available on the World Wide Web. The content of these sites is not controlled or endorsed in any way by the ISMRM or SMRT. Sections devoted to MR safety and MRI information for patients is also available. Study groups are established to foster interaction among members with a common interest in topical and active areas of MR. If you are a member of the ISMRM or SMRT, you may become a member of any number of study groups; however, the cost of membership for each study group is US20. Recorded educational presentations, oral presentations, traditional posters, and electronic posters Available only to Meeting registrants - Now online | biology, bookstore, collaboration, journals, magnetic resonance, medicine, mri, mr safety, newsletter, nmr, scientific association, study groups | grid.420361.2, ISNI: 0000 0001 2107 6555, nif-0000-10673 | https://ror.org/038wdy960 | SCR_001988 | ISMRM | 2026-02-14 02:00:12 | 3 | ||||||||
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Wellcome Trust Case Control Consortium Resource Report Resource Website 100+ mentions |
Wellcome Trust Case Control Consortium (RRID:SCR_001973) | WTCCC | data or information resource | Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2. | gene, genomic, genetics, microarray, genome-wide association study, snp, genome-wide association, blood, dna, genotype, variation, genome, sequence variant, copy number variation, genetic variation, phenotype, disease |
is related to: Psychiatric Genomics Consortium has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Bipolar disorder, Coronary artery disease, Crohn's disease, Rheumatoid arthritis, Type 1 diabetes, Type 2 diabetes, Hypertension, Control, Multiple sclerosis, Breast cancer, Ankylosing spondylitis, Autoimmune thyroid disease, Malaria, Tuberculosis, Inflammatory bowel disease, Barrett's esophagus, Esophageal adenocarcinoma, Glaucoma, Ischemic stroke, Pre-eclampsia, Parkinson's disease, Psychosis endophenotypes, Psoriasis, Schizophrenia, Ulcerative colitis, Visceral leishmaniasis, Primary biliary cirrhosis, Anorexia nervosa, Human immunodeficiency virus, Renal transplant dysfunction, Diabetes | Wellcome Trust ; Bill and Melinda Gates Foundation ; Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:17554300 | Access to summary data and individual-level genotype data is available by application to the Wellcome Trust Case Control Consortium Data Access Committee. Access to data will be granted to qualified investigators for appropriate use. | nif-0000-10551 | SCR_001973 | Wellcome Trust Case-Control Consortium (WTCCC) | 2026-02-14 02:00:12 | 213 | ||||
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NeuralAct Resource Report Resource Website 10+ mentions |
NeuralAct (RRID:SCR_002066) | NeuralAct | software resource | Software to visualize electrocorticographic (ECoG) and possibly also other kinds of neural activity (EEG / EMG/ DOT) on a 3D model of the cortical surface. The tool has been used to produce cortical activation images and image sequences in several recent studies using ECoG. The tool is written in matlab. The package is thoroughly documented and includes a demo. | brain, imaging, electrocorticographic, eeg, meg, dot, matlab, cortex, visualization, neural activity | NIH ; NIBIB EB006356; NIBIB EB000856; United States army research office W911NF-08-1-0216; United States army research office W911NF-07-1-0415 |
PMID:25381641 | Free, Available for download, Freely available | SciRes_000162 | http://www.neuralgate.org/software | SCR_002066 | NeuralAct: A tool to visualize cortical activity on a 3D model of the cortex | 2026-02-14 02:00:18 | 13 | |||||
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PurBayes Resource Report Resource Website 10+ mentions |
PurBayes (RRID:SCR_002068) | software resource | An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data. | software package, unix/linux, mac os x, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:23749958 | Free, Available for download, Freely available | biotools:purbayes, OMICS_03561 | https://bio.tools/purbayes | http://cran.r-project.org/web/packages/PurBayes/ | SCR_002068 | PurBayes: Bayesian Estimation of Tumor Purity and Clonality | 2026-02-14 02:00:18 | 10 | |||||
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XPP-Aut: X-Windows Phase Plane plus Auto Resource Report Resource Website 100+ mentions |
XPP-Aut: X-Windows Phase Plane plus Auto (RRID:SCR_001996) | software resource | XPPAUT is a tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations. It evolved from a chapter written by John Rinzel and me on the qualitative theory of nerve membranes and eventually became a commercial product for MSDOS computers called PHASEPLANE. It is now available as a program running under X11 and Windows. The code brings together a number of useful algorithms and is extremely portable. All the graphics and interface are written completely in Xlib which explains the somewhat idiosyncratic and primitive widgets interface. XPP contains the code for the popular bifurcation program, AUTO . Thus, you can switch back and forth between XPP and AUTO, using the values of one program in the other and vice-versa. I have put a ``friendly'' face on AUTO as well. You do not need to know much about it to play around with it. XPP has the capabilities for handling up to 590 differential equations. There are over a dozen solvers including several for stiff systems, a solver for integral equations and a symplectic solver. Up to 10 graphics windows can be visible at once and a variety of color combinations is supported. PostScript output is supported as well as GIF and animator GIF movies Post processing is easy and includes the ability to make histograms, FFTs and applying functions to columns of your data. Equilibria and linear stability as well as one-dimensional invariant sets can be computed. Nullclines and flow fields aid in the qualitative understanding of two-dimensional models. Poincare maps and equations on cylinders and tori are also supported. Some useful averaging theory tricks and various methods for dealing with coupled oscillators are included primarily because that is what I do for a living. Equations with Dirac delta functions are allowable. I have added an animation package that allows you to create animated versions of your simulations, such as a little pendulum moving back and forth or lamprey swimming. See toys! for examples. There is a curve-fitter based on the Marquardt-Levenberg algorithm which lets you fit data points to the solutions to dynamical systems. It is possible to automatically generate "movies'' of three-dimensional views of attractors or parametric changes in the attractor as some parameters vary. Dynamically link to external subroutines XPP has been successfully compiled on a SPARC II under OpenLook, a SPARC 1.5 running generic X, a NeXT running X11R4, a DEC 5000, a PC using Linux or Windows, and SGI and an HP 730. It also runs under Win95/NT/98 if you have an X-Server. I cannot vouch for other platforms but it has been compiled on the IBM RS6000. Building XPP requires only the standard C compiler, and Xlib. Look at the any README files that come with the distribution for solutions to common compilation problems. | functional equations, boundary value problems, delay equations, difference equations, differential equations, membranes, nerve, stochastic equations | has parent organization: University of Pittsburgh; Pennsylvania; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10767 | SCR_001996 | XPP as well as XPPAUT | 2026-02-14 02:00:21 | 193 | ||||||||
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TRAMS Resource Report Resource Website 1+ mentions |
TRAMS (RRID:SCR_002003) | TRAMS | software resource | A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs. | single nucleotide polymorphism, windows, python, mac os, linux, synonymous, non-synonymous, nonsense, annotate, genomic variation |
is listed by: OMICtools is related to: Galaxy has parent organization: FigShare |
PMID:23828175 | Free, Available for download, Freely available | OMICS_01924 | SCR_002003 | Tool for Rapid Annotation of Microbial SNPs, Tool for rapid annotation of microbial SNPs: a simple program for rapid annotation of genomic variation in prokaryotes, Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes, TRAMS: a simple program for rapid annotation of genomic variation in prokaryotes | 2026-02-14 02:00:16 | 1 | ||||||
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Vennt Resource Report Resource Website 1+ mentions |
Vennt (RRID:SCR_002083) | software resource | A web-tool to generate dynamic Venn diagrams for differential gene expression. | unix/linux, mac os x, windows, python | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_03549 | https://github.com/drpowell/vennt | SCR_002083 | Vennt - Dynamic Venn diagrams for Differential Gene Expression | 2026-02-14 02:00:22 | 7 |
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