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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Artinis Medical Systems Oxysoft Resource Report Resource Website 1+ mentions |
Artinis Medical Systems Oxysoft (RRID:SCR_024666) | software resource, software application | Software application used to collect, store, view, and analyse all necessary data from the Brite Family devices, PortaMon, PortaLite, OctaMon and OxyMon developed by Artinis Medical Systems and highly customisable to individual requirements. | Artinis Medical Systemscollect, store, view, analyse, Brite Family, PortaMon, PortaLite, OxyMon, devices data, | Restricted | SCR_024666 | 2026-08-12 10:53:11 | 3 | |||||||||||
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Core Life Sciences Resource Report Resource Website |
Core Life Sciences (RRID:SCR_000138) | material resource, instrument supplier | A commercial organization that supplies researchers with life science instruments, reagents and consumables, and lab services. | commercial, lab procedures, affymetrix DNA microarray, microRNA, methylation analysis, peptide microarray, quantitative PCR, reagent supplier, instrument supplier | is listed by: ScienceExchange | Public, Commercial, Institutional pricing is available | SciEx_10652 | http://www.scienceexchange.com/facilities/core-life-sciences-inc | SCR_000138 | Core Life Sciences Inc. | 2026-08-12 10:48:10 | 0 | |||||||
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Tecan i-Control Resource Report Resource Website 1+ mentions |
Tecan i-Control (RRID:SCR_024562) | software resource, software application | Microplate reader software as user friendly interface for control of Tecan's Infinite series of microplate readers designed for professional use. | Tecan, Infinite plate reader family system software, | Restricted | https://bif.wisc.edu/wp-content/uploads/sites/389/2017/11/i-control_Manual.pdf | SCR_024562 | i-Control, Tecan i-Control software | 2026-08-12 10:53:15 | 5 | |||||||||
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CPODES numerical integrator Resource Report Resource Website 1+ mentions |
CPODES numerical integrator (RRID:SCR_000766) | CPODES | software resource, source code | CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules. | dynamic, numerical integrator, multibody, source code |
uses: Simbody(tm): SimTK Multibody Dynamics Toolset is listed by: Simtk.org |
Free, Available for download, Freely available | nif-0000-23329 | SCR_000766 | 2026-08-12 10:48:16 | 6 | ||||||||
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JSU Environmental Toxicology Core Lab Resource Report Resource Website |
JSU Environmental Toxicology Core Lab (RRID:SCR_000884) | material resource, instrument supplier | A research laboratory and facility which supports research on environmental toxicology at Jackson State University. | environment, toxic, toxicology, equipment, instrument, technology |
is listed by: Eagle I has parent organization: Jackson State University; Mississippi; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156361 | SCR_000884 | Jackson State University Environmental Toxicology Lab | 2026-08-12 10:48:18 | 0 | ||||||||
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StereoCell v2.0 Resource Report Resource Website 1+ mentions |
StereoCell v2.0 (RRID:SCR_024438) | software resource, software application | Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries. | Register spatial gene expression map, register image, generating single cell gene expression profile, high resolution spatial transcriptomics, | Free, Available for download, Freely available | SCR_024438 | StereoCell | 2026-08-12 10:53:08 | 1 | ||||||||||
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MGH Center for Morphometric Analysis Resource Report Resource Website 10+ mentions |
MGH Center for Morphometric Analysis (RRID:SCR_000885) | material resource, instrument supplier | A center dedicated to developing and applying morphometric methods to biomedical imaging data such as high-resolution MRI. The lab uses automated and semi-automated software such that MRI brain images are segmented into anatomical regions of interest. Projects in both basic and applied brain research include research on strokes and tumors; medical image processing research includes shape analysis of anatomical brain regions and measurement and analysis of brain volumes. | brain, neuroscience, imaging, mri, magnetic resonance imaging, morphometric, biomedical, software, automated, anatomy | is listed by: Eagle I | nlx_156387 | http://harvard.eagle-i.net/i/0000012e-9721-d0fd-55da-381e80000000 | SCR_000885 | 2026-08-12 10:48:18 | 15 | |||||||||
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tacg Resource Report Resource Website |
tacg (RRID:SCR_024374) | software resource, software application | Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA. | pattern matching in biological strings, restriction enzyme analysis, | is listed by: Debian | PMID:11882250 | Free, Available for download, Freely available, | https://sources.debian.org/src/tacg/ | SCR_024374 | 2026-08-12 10:53:07 | 0 | ||||||||
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WHONET Resource Report Resource Website 10+ mentions |
WHONET (RRID:SCR_024495) | software resource, software application | Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide. | management and analysis of microbiology laboratory data | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024495 | 2026-08-12 10:53:05 | 30 | ||||||||||
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VelvetOptimiser Resource Report Resource Website 50+ mentions |
VelvetOptimiser (RRID:SCR_024376) | software resource, software application | Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile. | wrapper script, Velvet assembler, optimising assembly, optimum search, search supplied hash value range, optimum coverage cutoff, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_14601 | https://sources.debian.org/src/velvetoptimiser/ https://sources.debian.org/src/vsearch/ | SCR_024376 | velvetoptimiser, perl-velvetoptimiser | 2026-08-12 10:53:13 | 60 | |||||||
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PyEGA Resource Report Resource Website 1+ mentions |
PyEGA (RRID:SCR_024654) | software resource, software application | Software Python tool for viewing and downloading files from authorized European Genome-phenome Archive datasets. Python based EGA download client. | EGA download client, viewing and downloading files, European Genome-phenome Archive datasets, | Free, Available for download, Freely available | https://github.com/blachlylab/pyega | SCR_024654 | Python European Genome-phenome Archive | 2026-08-12 10:53:16 | 4 | |||||||||
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VisIt Resource Report Resource Website |
VisIt (RRID:SCR_024370) | software resource, software application | Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations. | generate visualizations, animation, analysis, save resulting images and animations for presentations, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/visit/ | SCR_024370 | visit | 2026-08-12 10:53:07 | 0 | ||||||||
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ImageTwin Resource Report Resource Website 1+ mentions |
ImageTwin (RRID:SCR_024543) | software resource, software application | AI based software for detecting integrity issues in figures of scientific articles. Used for detecting integrity issues in life science articles. Detects inappropriate manipulation and duplication in many figure types, including blots, microscopy images, and light photography. | scientific literature manipulated images check, detect inappropriate manipulation and duplication, blots check, microscopy images check, light photography check, manipulated images, | Restricted | SCR_024543 | 2026-08-12 10:53:09 | 3 | |||||||||||
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3D ImageJ Suite Resource Report Resource Website 1+ mentions |
3D ImageJ Suite (RRID:SCR_024534) | software resource, software application | Software suite provides plugins to enhance 3D capabilities of ImageJ. | enhance 3D capabilities of ImageJ, | works with: ImageJ | Free, Freely available | SCR_024534 | 2026-08-12 10:53:09 | 1 | ||||||||||
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Sequence Search and Alignment by Hashing Algorithm Resource Report Resource Website 1+ mentions |
Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) | SSAHA2 | software resource, source code | A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported. | sequence, genomic, analysis, search, alignment, algorithm, mapping, bio.tools |
is listed by: OMICtools is listed by: bio.tools is related to: SMALT has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11591649 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ssaha2, OMICS_00690, nlx_93831 | https://bio.tools/ssaha2 | SCR_000544 | ssaha2, ssaha, Sequence Search and Alignment by Hashing Algorithm | 2026-08-12 10:48:14 | 6 | |||||
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BioThings API Resource Report Resource Website |
BioThings API (RRID:SCR_024539) | software resource, software application | FAIR API ecosystem for inter-connected biomedical knowledge. Provides three components in its API development ecosystem: family of high-performance APIs for accessing up-to-date annotations for genes, genetic variants, chemicals and drugs; provides BioThings API packages its API-development best practice into reusable Software Development Kit to help other bioinformaticians to build same high-quality API to distribute their own specific knowledge; BioThings API provides platform to foster findability and interoperability across community developed biomedical APIs. Provides tools for authoring API metadata following community supported OpenAPI standard and hosts standardized interactive API documentation. Defines set of OpenAPI extensions to provide biomedical specific semantic annotations. | FAIR API ecosystem, inter-connected biomedical knowledge, biomedical entity type, biological knowledge space, biomedical APIs, Software Development Kit, authoring API metadata tools, OpenAPI extensions, | Free, Freely available | SCR_024539 | 2026-08-12 10:53:15 | 0 | |||||||||||
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BUSM Mass Spectrometry Resource Resource Report Resource Website |
BUSM Mass Spectrometry Resource (RRID:SCR_000823) | Mass Spectrometry Resource | training resource, biomedical technology research center | Biomedical technology research center that conducts high-sensitivity structural determinations and analyses of biological compounds via mass spectrometry. The emphasis is on glycoconjugates, oligosaccharides and proteins. | systems biology technology center, mass spectrometry, glycoconjugate, oligosaccharide, protein | has parent organization: Boston University School of Medicine; Massachusetts; USA | NCRR P41RR010888 | nlx_152679 | SCR_000823 | Mass Spectrometry Resource for Biology and Medicine, Boston University School of Medicine Mass Spectrometry Resource, Boston University Mass Spectrometry Resource for Biology and Medicine | 2026-08-12 10:48:17 | 0 | |||||||
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sprai Resource Report Resource Website |
sprai (RRID:SCR_024353) | software resource, software application | Software tool to correct sequencing errors in single pass reads for de novo assembly. | correct sequencing errors, single pass reads, de novo assembly, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21293 | https://sources.debian.org/src/sprai/ | SCR_024353 | single pass read accuracy improver | 2026-08-12 10:53:02 | 0 | |||||||
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scikit-learn-intelex Resource Report Resource Website 1+ mentions |
scikit-learn-intelex (RRID:SCR_024595) | software resource, software application | Software tool as Intel(R) Extension for Scikit-learn to speed up Scikit-learn application. Used to accelerate existing scikit-learn code. Accelerates Scikit-learn applications and still have full conformance with all Scikit-Learn APIs and algorithms. Software AI accelerator brings over 10-100X acceleration across variety of applications. | Intel(R) Extension, Scikit-learn, speed up Scikit-learn application, accelerate existing scikit-learn code, | Free, Available for download, Freely available | https://github.com/intel/scikit-learn-intelex/ | SCR_024595 | 2026-08-12 10:53:10 | 1 | ||||||||||
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streamlit Resource Report Resource Website 1+ mentions |
streamlit (RRID:SCR_024354) | software resource, software application | Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps. | turn data scripts into shareable web apps, build and share data apps, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/streamlit/ | SCR_024354 | 2026-08-12 10:53:12 | 9 |
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