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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-08-01 12:01:56 | 193 | ||||||||
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GapMis Resource Report Resource Website |
GapMis (RRID:SCR_001999) | software resource | A software tool for pairwise sequence alignment with a single gap. | standalone software | is listed by: OMICtools | PMID:22974258 | Free, Available for download, Freely available | OMICS_03692 | SCR_001999 | 2026-08-01 12:01:56 | 0 | ||||||||
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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 | 2026-08-01 12:02:07 | 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 | 2026-08-01 12:01:58 | 7 | |||||||
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TEQC Resource Report Resource Website 10+ mentions |
TEQC (RRID:SCR_001943) | software resource | An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on. | standalone software, unix/linux, mac os x, windows, r, genetics, microarray, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21398674 | Free, Available for download, Freely available | OMICS_03602 | SCR_001943 | TEQC - Quality control for target capture experiments | 2026-08-01 12:01:39 | 14 | |||||||
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flowViz Resource Report Resource Website 10+ mentions |
flowViz (RRID:SCR_002075) | software resource | Software that provides visualization tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18245128 | Free, Available for download, Freely available | OMICS_05615 | SCR_002075 | flowViz - Visualization for flow cytometry | 2026-08-01 12:01:42 | 30 | |||||||
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flowQB Resource Report Resource Website |
flowQB (RRID:SCR_002144) | software resource | A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05610 | http://www.bioconductor.org/packages/release/bioc/html/flowQB.html | SCR_002144 | B and CVinstrinsic calculations, flowQB - Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q | 2026-08-01 12:01:42 | 0 | |||||||
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Leica: TCS SPE Resource Report Resource Website 10+ mentions |
Leica: TCS SPE (RRID:SCR_002140) | TCS SPE | instrument resource | High resolution, compact and robust confocal that enables immunohistochemical colocalization analysis of florescent markers. Leica TCS SPE confocal point-scanning, spectral system for fluorescence imaging of live or fixed cells. | confocal microscope, imaging, instrument, equipment, hardware | has parent organization: Leica Microsystems | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_002140.pdf | SciRes_000154 | http://www.leica-microsystems.com/fileadmin/downloads/Leica%20TCS%20SPE/Brochures/Leica%20TCS%20SPE-Brochure_EN.pdf | SCR_002140 | Leica TCS SPE confocal microscope | 2026-08-01 12:01:42 | 32 | |||||
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miso-lims Resource Report Resource Website 10+ mentions |
miso-lims (RRID:SCR_002259) | MISO | software resource | Open source software for a Laboratory Information Management System (LIMS) for NGS sequencing centres. | laboratory information management system, ngs sequencing, lims | is listed by: OMICtools | Open Source, Free | OMICS_01007 | SCR_002259 | MISO: An open-source LIMS for NGS sequencing centres, MISO: An open source LIMS for small-to-large scale sequencing centres | 2026-08-01 12:01:44 | 20 | |||||||
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University of Alaska Fairbanks; Alaska; USA Resource Report Resource Website |
University of Alaska Fairbanks; Alaska; USA (RRID:SCR_002251) | UAF | university | Public research university in Fairbanks, Alaska that offers degree programs in engineering, liberal arts, fisheries and ocean sciences, and rural and community development. | university in alaska, fisheries, ocean sciences, rural and community development, engineering |
is parent organization of: Alaska Climate Research Center is parent organization of: Alaska Satellite Facility is parent organization of: UAF Alaska Stable Isotope Facility is parent organization of: UAF Animal Quarters Core Laboratory is parent organization of: UAF Community Engagement and Clinical Support Core is parent organization of: UAF DNA Core Laboratory is parent organization of: UAF Epidemiology and Biostatistics Core Laboratory is parent organization of: UAF Nutrition and Physical Activity Core is parent organization of: UAF Optical and Tissue Culture Core is parent organization of: University of Alaska Fairbanks Genomics Core Facility |
Public | grid.70738.3b, Crossref funder ID:100005921, nlx_156102, ISNI:0000 0004 1936 981X, Wikidata:Q1285262 | https://ror.org/01j7nq853 | SCR_002251 | University of Alaska Fairbanks, UA Fairbanks | 2026-08-01 12:02:02 | 0 | ||||||
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Kindai University School of Medicine; Osaka; Japan Resource Report Resource Website |
Kindai University School of Medicine; Osaka; Japan (RRID:SCR_002258) | university | Medical school division of Kindai University with a resident-centered approach to medicine. | medical school in japan, resident centered medicine |
has parent organization: Kindai University; Osaka; Japan is parent organization of: BrainStars |
nlx_149307 | http://nasc.in/ocenia/index.php?option=com_content&view=article&id=28:kinki-university-school-of-medicine-&catid=1:japan | SCR_002258 | Kinki University School of Medicine | 2026-08-01 12:02:02 | 0 | ||||||||
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flowFit Resource Report Resource Website 1+ mentions |
flowFit (RRID:SCR_002286) | software resource | A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24681909 | Artistic License, v2 | OMICS_05601 | SCR_002286 | flowFit - Estimate proliferation in cell-tracking dye studies | 2026-08-01 12:02:03 | 4 | |||||||
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Tokyo Metropolitan Institute of Medical Science; Tokyo; Japan Resource Report Resource Website |
Tokyo Metropolitan Institute of Medical Science; Tokyo; Japan (RRID:SCR_002203) | institution | Scientific institute in Japan that promotes project-based research, targeted research initiatives for clinically-relevant questions on cancer, and dissemination of information to the research community and public. | research promotion, institute of science, scientific institute in japan | is parent organization of: Digital Brain Atlas of the Common Marmoset | Free, Freely available | grid.272456.0, nlx_144090 | https://ror.org/00vya8493 | http://rinshoken.igakuken.or.jp/eng/index_e.html | SCR_002203 | Tokyo Metropolitan Institute of Medical Science, RINSHOKEN | 2026-08-01 12:02:01 | 0 | ||||||
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spliceR Resource Report Resource Website 10+ mentions |
spliceR (RRID:SCR_002280) | software resource | An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. | standalone software, unix/linux, mac os x, windows, c, r, differential expression, high throughput sequencing, rna-seq, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24655717 | GNU General Public License, v2 or greater | OMICS_03514 | SCR_002280 | spliceR - Classification of alternative splicing and prediction of coding potential from RNA-seq data | 2026-08-01 12:01:45 | 25 | |||||||
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neuRosim Resource Report Resource Website 10+ mentions |
neuRosim (RRID:SCR_002154) | neuRosim | software resource | Software package that allows users to generate fMRI time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments. | r, fmri, time series, 4d | has parent organization: CRAN | Free, Available for download, Freely available | SciRes_000194 | SCR_002154 | neuRosim: Functions to Generate fMRI Data Including Activated Data Noise Data and Resting State Data | 2026-08-01 12:02:08 | 20 | |||||||
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BD Biosciences: LSR II Flow Cytometer Resource Report Resource Website 10+ mentions |
BD Biosciences: LSR II Flow Cytometer (RRID:SCR_002159) | LSR II Flow Cytometer | instrument resource | Benchtop high-performance cell sorter with multiple lazer, detector and fluoroscrome options. Allows detection of 12 parameters (10 color conjugates, forward and sideward scatter). | flow cytometer, instrument, equipment, hardware | has parent organization: BD Biosciences | THIS RESOURCE IS NO LONGER IN SERVICE | https://drive.google.com/file/d/1iqsXa8XNCYWutCswBRYBWluHGag0lOSx/view?usp=drivesdk | Model_Number_BD LSR II, SciRes_000152 | https://fccf.sitehost.iu.edu/pdf/BDLSRIIUserGuide.pdf | http://www.rockefeller.edu/fcrc/pdf/BD_LSRII_Brochure_SJ-0142-00.pdf | SCR_002159 | 2026-08-01 12:02:00 | 35 | |||||
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FR-HIT Resource Report Resource Website 10+ mentions |
FR-HIT (RRID:SCR_002181) | FR-HIT | software resource | An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit. | metagenomics, bioinformatics, sequence analysis, next-generation sequencing |
is listed by: OMICtools has parent organization: Google Code |
Free, Freely available | OMICS_01850 | SCR_002181 | FR-HIT: Metagenome Fragment Recruitment at High Identity with Tolerance, Metagenome Fragment Recruitment at High Identity with Tolerance, Fragment Recruitment at High Identity with Tolerance | 2026-08-01 12:02:08 | 11 | |||||||
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flowPlots Resource Report Resource Website |
flowPlots (RRID:SCR_002177) | software resource | Software for analysis plots and data class for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, data representation, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05608 | SCR_002177 | flowPlots: analysis plots and data class for gated flow cytometry data | 2026-08-01 12:02:00 | 0 | ||||||||
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metaRNASeq Resource Report Resource Website 10+ mentions |
metaRNASeq (RRID:SCR_002174) | software resource | Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: SMAGEXP has parent organization: CRAN |
PMID:24678608 | Free, Available for download, Freely available | OMICS_03527 | SCR_002174 | metaRNASeq: Meta-analysis of RNA-seq data | 2026-08-01 12:02:08 | 30 | |||||||
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UCL Medical School; London; United Kingdom Resource Report Resource Website |
UCL Medical School; London; United Kingdom (RRID:SCR_002211) | university | Medical school at the University College London that provides undergraduate and postgraduate medical education programs, educational research, and specializations in variety of medical subfields. | medical school, london, medical education research |
has parent organization: University College London; London; United Kingdom is parent organization of: UCL-RFH BioBank |
Free | nlx_143837 | SCR_002211 | University College London Medical School, UCL Medical School | 2026-08-01 12:02:01 | 0 |
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