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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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epitopepredict Resource Report Resource Website 1+ mentions |
epitopepredict (RRID:SCR_019221) | simulation software, software resource, software application | Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported. | Protein sequence, MHC binding prediction, whole genomes, multiple target MHC allele, epitope prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:epitopepredict | https://epitopepredict.readthedocs.io/en/latest/, https://bio.tools/epitopepredict | SCR_019221 | 2026-08-12 10:52:13 | 2 | ||||||||
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MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | simulation software, software resource, software application | Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools |
is listed by: bio.tools is listed by: Debian |
Institutional Research Fund of IISER Bhopal | PMID:24736651 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mp3 | https://bio.tools/mp3 | SCR_019282 | MP3 | 2026-08-12 10:52:24 | 2 | |||||
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RNAProt Resource Report Resource Website 1+ mentions |
RNAProt (RRID:SCR_021218) | simulation software, software resource, software application | Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction. | RBP, RNA Binding Protein, RNA sequences, protein binding preferences, predict RPB binding sites, neural networks |
is related to: Conda is related to: BioConda |
Free, Available for download, Freely available | SCR_021218 | 2026-08-12 10:52:32 | 1 | ||||||||||
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NPSV Resource Report Resource Website 1+ mentions |
NPSV (RRID:SCR_020984) | simulation software, software resource, software application | Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline. | WGS data, short read, whole genome sequencing data, standalone genotyping, insertion structural variants, deletion structural variants, structural variants, SV genotyping, NGS simulation | Free, Available for download, Freely available | SCR_020984 | Non-Parametric Structural Variant Genotyper, Non-Parametric Structural Variant genotyper | 2026-08-12 10:52:26 | 1 | ||||||||||
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HDMF Common Schema Resource Report Resource Website |
HDMF Common Schema (RRID:SCR_021342) | data or information resource, narrative resource, standard specification | Software tool to define collection of common, reusable data structures that build foundation for modeling of advanced data formats and is integrated with HDMF.Provided data structures include DynamicTable, VectorData, VectorIndex, ElementIdentifiers, DynamicTableRegion, AlignedDynamicTable and CSRMatrix. | Schema, data standard, neurophysiology data standard, DynamicTable, VectorData, VectorIndex, ElementIdentifiers, DynamicTableRegion, AlignedDynamicTable, CSRMatrix |
is related to: Neurodata Without Borders is related to: Hierarchical Data Modeling Framework is related to: PyNWB is related to: MatNWB |
DOI:10.1109/BigData47090.2019.9005648 | Free, Available for download, Freely Available | https://hdmf-common-schema.readthedocs.io | SCR_021342 | hdmf common schema | 2026-08-12 10:52:34 | 0 | |||||||
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Vascular Access Society of the Americas Resource Report Resource Website |
Vascular Access Society of the Americas (RRID:SCR_004058) | VASA | data or information resource, community building portal, portal | Society devoted to the advancement of the field of dialysis access through research, education and advocacy for patients with end stage kidney disease. They provide vascular access education for physicians, nurses, and other health care professionals and advocate for evidenced-based best clinical practices. | dialysis, kidney, clinical, vascular | is related to: Kidney Health Initiative | End stage kidney disease | nlx_158492 | SCR_004058 | 2026-08-12 10:48:55 | 0 | ||||||||
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SHared Access Research Ecosystem Resource Report Resource Website |
SHared Access Research Ecosystem (RRID:SCR_004125) | SHARE | data or information resource, community building portal, portal | A higher education and research community initiative to ensure the preservation of, access to, and reuse of research outputs. SHARE will develop solutions that capitalize on the compelling interest shared by researchers, libraries, universities, funding agencies, and other key stakeholders to maximize research impact, today and in the future. SHARE aims to make the inventory of research assets more discoverable and more accessible, and to enable the research community to build upon these assets in creative and productive ways. ARL, AAU, and APLU strongly believe that ensuring broad and continuing access to research is central to the mission of higher education. Research publications, research data, other research outputs, along with their associated metadata, should be publicly accessible and available for reuse, text mining, data mining, and machine reading. This accelerates further research and discovery. | library, data preservation, data access, data reuse, data sharing, metadata | Institute of Museum and Library Services ; Alfred P. Sloan Foundation |
nlx_158608 | SCR_004125 | SHared Access Research Ecosystem (SHARE) | 2026-08-12 10:48:55 | 0 | ||||||||
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International Alliance of Patients Organizations Resource Report Resource Website |
International Alliance of Patients Organizations (RRID:SCR_004073) | IAPO | data or information resource, community building portal, portal | A global alliance representing patients of all nations across all disease areas and promoting patient-centered healthcare across the world. They represent people who suffer from diseases, disabilities, illnesses, impairments or syndromes and work with communities of patients to get their voices heard by all involved in healthcare. With the help of their members and collaborating organizations, they work towards patient-centered healthcare throughout the world. | healthcare | is related to: GetReal | nlx_158518 | SCR_004073 | International Alliance of Patients'' Organizations | 2026-08-12 10:48:55 | 0 | ||||||||
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Mouse Brain Architecture Project Resource Report Resource Website 1+ mentions |
Mouse Brain Architecture Project (RRID:SCR_004683) | data or information resource, atlas, reference atlas, d spatial image | An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset. | atlas, brain, brain architecture, connectivity, mouse brain architecture, neuroanatomy |
is related to: Brain Architecture Project has parent organization: Brain Architecture Project |
NIH Office of the Director ; NIMH RC1MH088659; NIMH R01MH087988 |
Fully accessible to the neuroscience community as well as interested members of the general public, Acknowledgement requested | nlx_146201 | http://www.brainarchitecture.org | http://www.brainarchitecture.org/mouse/about | SCR_004683 | MBA Project, Mouse Brain Architecture | 2026-08-12 10:49:01 | 5 | |||||
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Code4Lib Journal WordPress Customizations Resource Report Resource Website |
Code4Lib Journal WordPress Customizations (RRID:SCR_004798) | authoring tool, software resource, software application | WordPress plugins for Anti-Spam, Metadata, Presentation, URLs, and Workflow from the Code4Lib community, a group of computer programmers and library technologists who largely work for and with libraries. Anti-Spam *Akimset - Filters out spam-link comments based on their content *reCAPTCHA - Requires users to copy a distorted word before they can comment Metadata *COinS Quicktags Button - In the non-WYSIWYG editor, can be used to build a basic COinS tag. This has been abandoned in favor of the generator at http://generator.ocoins.info/. *unAPI Server - Provides information about articles. Useful for Zotero users. Presentation *SyntaxHighlighter - Makes code pretty. *C4LJ Custom the_author()- Replaces the text returned by the_author() with the value of the author custom field. Necessary since articles are entered by their editors, but we want author information to appear on the articles and in the syndication feeds. URLs *C4LJ Remove Parents - A customization of http://wordpress.org/extend/plugins/remove-parents/. Prettifies category URLs so that issues appear at http://journal.code4lib.org/issues/issue1 instead of http://journal.code4lib.org/issues/issues/issue1. *FeedBurner FeedSmith - Redirects the main feed and the general comments feed to FeedBurner Workflow *Issue Manager - Enables one-click publishing of new issues, and prevents articles from being published until their associated issue is published. *Role Manager - Allows creation of custom roles and editing of roles' permissions. Used to create the Reviewer role, which can read Private articles, so that authors can see their articles before publication, and to prevent editors from publishing articles on accident. | metadata, workflow, wordpress |
is listed by: FORCE11 is related to: WordPress |
nlx_79075 | https://www.force11.org/node/4734 | SCR_004798 | 2026-08-12 10:49:02 | 0 | |||||||||
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The Nervous System in Action Resource Report Resource Website |
The Nervous System in Action (RRID:SCR_004985) | Nervous System in Action | data or information resource, narrative resource, book | The Nervous System In Action by Michael D. Mann, Ph.D. is a textbook on nervous system physiology. Available here is the web accessible version of of this textbook. An Adobe Acrobat (PDF) version is also supplied for better printing. You will need Acrobat Reader to see and print it. The textbook consists of the following: Preface (1) Neurophysiology, An Overview (2) Human Behavior (3) 1. Diffusion and Transport (4) 2. Control Systems and Homeostasis (5) 3a. Properties of Excitable Membranes: The Membrane Potential (6) 3b. Properties of Excitable Membranes: The Spike (7) 4a. Receptor Properties: Receptor Potentials and Coding (8) 4b. Sensory Receptors II (9) 5. Somesthesia--Peripheral Mechanisms (0) 6. Somesthesia--Central Mechanisms (a) 7. Vision (b) 8. Audition (c) 9. The Vestibular System (d) 10.Gustatory and Olfactory Senses (e) 11. Muscle Receptors (f) 12. Peripheral Nerves (g) 13. Synapses (h) 14. Muscle Contraction (i) 15. Reflexes (j) 16. Initiation and Control of Movement (k) 17. Activities Involving the Cerebral Hemispheres (l) 18. The Clinical Implications of Neurophysiological Concepts (m) 19. Learning and Memory Appendix: Common abbreviations (n) Glossary (o) Index (p) | neurophysiology, textbook, freely accessible textbook, nervous system | nlx_143992 | SCR_004985 | 2026-08-12 10:49:05 | 0 | ||||||||||
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Brodmann Areas in the Human Brain with an Emphasis on Vision and Language Resource Report Resource Website 1+ mentions |
Brodmann Areas in the Human Brain with an Emphasis on Vision and Language (RRID:SCR_004857) | Brodmann Areas in the Human Brain | data or information resource, atlas, reference atlas, data set | Reference atlas of Brodmann Areas in the Human Brain with an Emphasis on Vision and Language. Other Pages include: Flat Brodmann Maps, Brodmann Area Names (with locational Descriptions), Flat Visual Area Maps, Language Areas, PopUp Gyri Maps | brain, human, brodmann partition scheme region, vision, language, brodmann | has parent organization: University of Colorado; Colorado; USA | nlx_144391 | SCR_004857 | Brodmann Areas in the Human Brain with an Emphasis on Vision Language | 2026-08-12 10:49:03 | 2 | ||||||||
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Protocol Online - Your labs reference book Resource Report Resource Website 10+ mentions |
Protocol Online - Your labs reference book (RRID:SCR_004937) | Protocol Online | data or information resource, narrative resource, experimental protocol | Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert). | bioinformatics, molecular biology, immunology, microbiology, proteomics, cell biology, database |
is used by: NIF Data Federation is used by: Integrated Blogs |
Eppendorf ; Invitrogen ; Chang Bioscience ; Mirus ; KPL ; Oligomaster ; Abcam ; Nature Publishing Group |
nlx_90492 | SCR_004937 | Protocol Online Your lab''s reference book, Protocol-Online | 2026-08-12 10:49:04 | 11 | |||||||
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MRI Research Safety and Ethics Resource Report Resource Website |
MRI Research Safety and Ethics (RRID:SCR_005642) | MRI Research Safety and Ethics | data or information resource, narrative resource, standard specification | NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities. | mri, research, neuroscience, imaging | has parent organization: National Institute of Mental Health | NIMH | nlx_146267 | SCR_005642 | MRI Research Safety and Ethics: Points to Consider, MRI Research Safety Ethics | 2026-08-12 10:49:12 | 0 | |||||||
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Google Docs Resource Report Resource Website 10+ mentions |
Google Docs (RRID:SCR_005886) | Docs, Drive | authoring tool, service resource, software resource, software application | Authoring tool to create, share, and collaborate on the web with documents, spreadsheets, presentations, and more in real time. All your changes are saved automatically in Drive. | document, spreadsheet, presentation, drawing, form, slide, collaborate, authoring |
is used by: Paperpile is listed by: FORCE11 is related to: Paperpile |
Free, Public | nlx_149451 | http://www.force11.org/node/4693 | https://accounts.google.com/ServiceLogin?service=writely&passive=1209600&continue=https://docs.google.com/%23&followup=https://docs.google.com/ |
SCR_005886 | Google Drive | 2026-08-12 10:49:18 | 26 | |||||
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Universal Numerical Fingerprint Resource Report Resource Website |
Universal Numerical Fingerprint (RRID:SCR_005912) | UNF | data or information resource, narrative resource, standard specification | Citation standard that offers proper recognition to authors as well as permanent identification through the use of global, persistent identifiers in place of URLs, which can change frequently. Use of universal numerical fingerprints (UNFs) guarantees to the scholarly community that future researchers will be able to verify that data retrieved is identical to that used in a publication decades earlier, even if it has changed storage media, operating systems, hardware, and statistical program format. | identifier, universal numerical fingerprint, data citation |
is listed by: FORCE11 has parent organization: Dataverse Network Project |
nlx_149488 | SCR_005912 | Standard: Universal Numerical Fingerprint, The Standard: Universal Numerical Fingerprint | 2026-08-12 10:49:16 | 0 | ||||||||
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ORNL DAAC Data Product Citation Policy Resource Report Resource Website |
ORNL DAAC Data Product Citation Policy (RRID:SCR_005902) | ORNL DAAC Data Product Citation Policy | data or information resource, narrative resource, standard specification | Data Product Citation Policy of including a bibliographic citation for the products that were used in publications to acknowledge the scientists who have provided archived ORNL DAAC (Oak Ridge National Laboratory Distributed Active Archive Center) data products. Such citations will help others find the products and see how they have been used. Citation information is provided in the documentation that accompanies all data products. ORNL DAAC is operated by the ORNL Environmental Sciences Division and is responsible for data archival, product development and distribution, and user support for biogeochemical and ecological data and models. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemcial dynamics is one of the NASA Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project, which is responsible for providing scientific and other users access to data from NASA''s Earth Science Missions. | data citation, bibliographic citation |
is listed by: FORCE11 has parent organization: Oak Ridge National Laboratory |
nlx_149492 | SCR_005902 | Oak Ridge National Laboratory Distributed Active Archive Center Data Product Citation Policy | 2026-08-12 10:49:18 | 0 | ||||||||
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Retroviral Tagged Cancer Gene Database Resource Report Resource Website 10+ mentions |
Retroviral Tagged Cancer Gene Database (RRID:SCR_007908) | RTCGD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of high throughput insertional mutagenesis screening projects of retroviral and transposon insertional mutagenesis in mouse tumors. Information in the RTCGD is obtained from sequence comparison by using public databases UCSC genome mm9 browser. Data based on previous genome assembly mm8 is also available at RTCGD mm8. MCGP has developed three web search tools including Easy Search to query proviral integration sites using mouse gene symbol of gene name; Model Search to obtain RIS information based on tumor models and/or tumor types; Interaction Search to find gene-to-gene interaction. It displays the list of genes which reside in the same tumor to your gene of interest. | insertional mutagenesis screening, retroviral and transposon insertional mutagenesis, mouse tumors, |
has parent organization: NCI-Frederick has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03429, SCR_008568, nif-0000-31455 | http://rtcgd.ncifcrf.gov/ | SCR_007908 | RTCGD - Retroviral Tagged Cancer Gene Database | 2026-08-12 10:49:48 | 11 | ||||||
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R/TDTHAP Resource Report Resource Website 1+ mentions |
R/TDTHAP (RRID:SCR_007625) | software resource, software application | Software package for TDT with extended haplotypes in the R language. R is the public domain dialect of S. It should be possible to port this library to the commercial Splus product. The main problem would be translation of the help files. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/splus | is listed by: Genetic Analysis Software | nlx_154676, nlx_154602, SCR_000851 | http://www-gene.cimr.cam.ac.uk/clayton/software/ | SCR_007625 | TDTHAP | 2026-08-12 10:49:44 | 1 | ||||||||
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SimTKCore Resource Report Resource Website |
SimTKCore (RRID:SCR_008268) | SimTKCore | simulation software, software resource, software application | SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications. | computational algorithm, high-performance, linear algebra, numerical integration, numerical method, optimization, monte carlo sampling, multibody dynamics, molecular force field evaluation, nonlinear root finding, optimizing, cpodes, simbody, ipopt, molmodel, mit license, linux, mac os x, windows |
is listed by: Biositemaps has parent organization: Stanford University; Stanford; California has parent organization: Simtk.org |
NIGMS U54 GM072970 | PMID:20107615 | nif-0000-23310 | SCR_008268 | 2026-08-12 10:49:46 | 0 |
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