Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NetMODE Resource Report Resource Website 1+ mentions |
NetMODE (RRID:SCR_012085) | software resource | Fast motif detection algorithm for subgraph size no more than 6. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23272055 | OMICS_05019 | SCR_012085 | 2026-09-05 06:27:20 | 1 | |||||||||
|
SketchEl Resource Report Resource Website |
SketchEl (RRID:SCR_012082) | software resource | An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. | applet, mac os x, unix/linux, windows, java, javascript |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04982 | SCR_012082 | 2026-09-05 06:27:20 | 0 | |||||||||
|
HopeMap Resource Report Resource Website |
HopeMap (RRID:SCR_012081) | software resource | A connected-components based fast algorithm for network alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23710435 | OMICS_04896 | SCR_012081 | 2026-09-05 06:27:20 | 0 | |||||||||
|
MCDL Resource Report Resource Website 1+ mentions |
MCDL (RRID:SCR_012084) | software resource | A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. | applet, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05001 | SCR_012084 | 2026-09-05 06:27:20 | 2 | ||||||||||
|
GLARE Resource Report Resource Website 1+ mentions |
GLARE (RRID:SCR_012083) | software resource | A software that facilitates and improves the design of chemical combinatorial libraries. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20981532 | Free, Public | OMICS_04992 | SCR_012083 | Global Library Assessment of REagents | 2026-09-05 06:27:20 | 5 | |||||||
|
MFPaQ Resource Report Resource Website 10+ mentions |
MFPaQ (RRID:SCR_012049) | software resource | Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison). | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:17533220 | biotools:mfpaq, OMICS_02495 | https://bio.tools/mfpaq | SCR_012049 | Mascot File Parsing and Quantification | 2026-09-05 06:27:19 | 14 | |||||||
|
ProteoWizard Resource Report Resource Website 1000+ mentions |
ProteoWizard (RRID:SCR_012056) | software resource | Software that enables rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. | standalone software, c++ |
is listed by: OMICtools is related to: Skyline has parent organization: SourceForge |
PMID:23051804 | Apache License | OMICS_03354 | SCR_012056 | 2026-09-05 06:27:19 | 3729 | ||||||||
|
ADTEx Resource Report Resource Website 50+ mentions |
ADTEx (RRID:SCR_012059) | software resource | A software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. | standalone software, python, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23368785 | GNU General Public License | OMICS_03365 | SCR_012059 | 2026-09-05 06:27:20 | 95 | ||||||||
|
multiplierz Resource Report Resource Website 1+ mentions |
multiplierz (RRID:SCR_012058) | software resource | An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19874609 | GNU Lesser General Public License | biotools:multiplierz, OMICS_03360 | https://bio.tools/multiplierz | SCR_012058 | 2026-09-05 06:27:19 | 7 | |||||||
|
TE-locate Resource Report Resource Website 1+ mentions |
TE-locate (RRID:SCR_012063) | software resource | A software tool to locate all copies of sequences in a reference sequence using read-pairs. | java, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24832231 | OMICS_03507 | SCR_012063 | 2026-09-05 06:27:19 | 1 | |||||||||
|
LAITOR Resource Report Resource Website 1+ mentions |
LAITOR (RRID:SCR_012101) | software resource | A text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20122157 | GNU General Public License | OMICS_05240 | SCR_012101 | 2026-09-05 06:27:20 | 1 | ||||||||
|
MatNMR Resource Report Resource Website 10+ mentions |
MatNMR (RRID:SCR_012060) | software resource | A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17448713 | OMICS_03375 | SCR_012060 | 2026-09-05 06:27:19 | 16 | |||||||||
|
MZmine Resource Report Resource Website 500+ mentions |
MZmine (RRID:SCR_012040) | software resource | Software for mass-spectrometry data processing, with the main focus on LC-MS data. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20650010 | Open unspecified license | OMICS_02385 | SCR_012040 | 2026-09-05 06:27:18 | 964 | ||||||||
|
ORCA Resource Report Resource Website 1000+ mentions |
ORCA (RRID:SCR_012097) | software resource | A Matlab package extending the scope of established COBRA metabolic modelling. | software package, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24336807 | Free for academic use | OMICS_05191 | SCR_012097 | 2026-09-05 06:27:21 | 1540 | ||||||||
|
COBRApy Resource Report Resource Website 100+ mentions |
COBRApy (RRID:SCR_012096) | software resource | Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods. | software package, mac os x, unix/linux, windows, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23927696 DOI:10.1186/1752-0509-7-74 |
OMICS_05190, biotools:cobrapy | https://bio.tools/cobrapy | https://sources.debian.org/src/python3-cobra/ | SCR_012096 | COBRA for Python | 2026-09-05 06:27:20 | 341 | ||||||
|
Knowtator Resource Report Resource Website 10+ mentions |
Knowtator (RRID:SCR_012099) | software resource | A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system. | plugin |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05234 | SCR_012099 | 2026-09-05 06:27:20 | 11 | ||||||||||
|
PBJelly Resource Report Resource Website 100+ mentions |
PBJelly (RRID:SCR_012091) | software resource | Software that automates the finishing process using long sequence reads in a reference-guided assembly process. | standalone software, roche, pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23185243 | OMICS_05098 | SCR_012091 | 2026-09-05 06:27:20 | 172 | |||||||||
|
Mindtouch DekiWiki Resource Report Resource Website 1+ mentions |
Mindtouch DekiWiki (RRID:SCR_003425) | MindTouch | commercial organization, software resource, source code | A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more. | authoring, publishing, standard, web service, cloud |
is listed by: FORCE11 is listed by: Biositemaps has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Free, Freely available | nif-0000-33097 | http://sourceforge.net/projects/dekiwiki/, https://www.force11.org/node/4733 | SCR_003425 | MindTouch Core, DekiWiki, MindTouch Deki Wiki, Deki Wiki, MindTouch (frmly deki wiki) | 2026-09-05 06:25:03 | 2 | ||||||
|
MIAPA Resource Report Resource Website 1+ mentions |
MIAPA (RRID:SCR_003777) | MIAPA | data or information resource, narrative resource, standard specification | Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard. | phylogeny, dna, amino acid sequence |
is listed by: Minimum Information for Biological and Biomedical Investigations is listed by: GitHub is listed by: SourceForge |
PMID:16901231 | nlx_158100 | https://github.com/miapa/miapa/blob/master/checklist/MIAPA-checklist.md, http://mibbi.sourceforge.net/projects/MIAPA.shtml | SCR_003777 | Minimal Information for a Phylogenetic Analysis | 2026-09-05 06:25:08 | 1 | ||||||
|
SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_004013) | software resource | A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation. | c++, mrna-seq, qt |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15746290 PMID:14988116 |
GNU General Public License v2 | OMICS_01289 | SCR_004013 | 2026-09-05 06:25:13 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the Kravitz Resources search. From here you can search through a compilation of resources used by Kravitz and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that Kravitz has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on Kravitz then you can log in from here to get additional features in Kravitz such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into Kravitz you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
