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https://simtk.org

A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

Proper citation: Simtk.org (RRID:SCR_002680) Copy   

•   Source: SciCrunch Registry
  

https://simtk.org/home/simvascular

Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC.

Proper citation: SimVascular (RRID:SCR_002686) Copy   

•   Source: SciCrunch Registry
  

https://simtk.org/home/cv-gmodels

Repository of geometric models collected from on-going and past research projects in the Cardiovascular Biomechanics Research Laboratory at Stanford University. The geometric models are mostly built from imaging data of healthy and diseased individuals. For each of the models, a short description is given with a reference. The geometric models are in VTK PolyData XML .vtp format. * Audience: Biomechanical and computational researchers interested in complex models of cardiovascular applications * Long Term Goals and Related Uses: Allow users to download geometric models for cardiovascular applications. These geometric models can be used for research purposes, such as meshing and scientific visualization. Users are welcome to contact the project administrator, join the project and contribute additional models.

Proper citation: Cardiovascular Model Repository (RRID:SCR_002679) Copy   

•   Source: SciCrunch Registry
  

http://cran.r-project.org/web/packages/FisHiCal/

Software that integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.

Proper citation: FisHiCal (RRID:SCR_002799) Copy   

•   Source: SciCrunch Registry
  

https://github.com/SciCrunch/RRID-Instruments/blob/main/PDF/SCR_002677.pdf

Digital image processing system where microscope settings and processing steps may be adjusted in single user interface. Can acquire images from variety of cameras. Includes software package for capturing, archiving and preparing images for publication. Allows users to visualize and present images in several dimensions. Functionality of imaging toolbox expands constantly with wide range of different modules that are tailored to specific applications or microscope accessories.

Proper citation: Zeiss: AxioVision Imaging System (RRID:SCR_002677) Copy   

•   Source: SciCrunch Registry
  

Ratings or validation data are available for this resource

http://www.graphpad.com/

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

Proper citation: GraphPad Prism (RRID:SCR_002798) Copy   

•   Source: SciCrunch Registry
  

http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

•   Source: SciCrunch Registry
  

http://www.unidesign.ch/wiki/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 6, 2012. Connectome Wiki is a knowledge base for macro- and mesoscale brain region and brain structural connectivity information across species. Employing modern semantic wiki technology, it serves as collaborative platform as well. What can I get? * Brain Regions: Plenty of information, including links to relevant literature and much more. * Brain Connections: Well established neuronal connections based mainly on neuronal tracer studies from the literature. * Abbreviations: Look up abbreviations and corresponding English and Latin names * Partition Schemes: Foundational and more partitions with their corresponding delineation criteria and protocols. * Species: Information about different species is available, using their binomial name as identifier. * External: Enhance the ConnectomeViewer with Volume-To-Ontology mappings. * Data Source: You can download the raw data in RDF or JSON. How can I contribute? If your research is in particular brain regions, or model organisms not yet registered, feel free to act as domain expert and add your knowledge. If you do any tracer studies, add findings with appropriate published papers. Incrementally building a mesoscale skeleton wiring diagram. Complete anything that is missing. See also PapersToAdd. Register your own partition scheme and link it semantically against known schemes. Adding brain region pages for your particular research organisms. Use ConnectomeWiki as knowledge backend for your application concerned with gross neuroanatomy. The goals of this wiki are: * A collaborative platform to collect, collate, manage and disseminate mesoscale nervous system region and connectivity information across various species * Authority for Brain Region Abbreviations * Representation of Brain Region Homologies * Interrelation of Brain Partition Schemes * Information source for the ConnectomeViewer application

Proper citation: Connectome Wiki (RRID:SCR_002675) Copy   

•   Source: SciCrunch Registry
  

https://github.com/alibashir/pacmonstr

Software that implements a reference-based probabilistic approach to identify the Tandem Repeat (TR) region and estimate the number of these TR elements in long DNA reads.

Proper citation: PacmonSTR (RRID:SCR_002796) Copy   

•   Source: SciCrunch Registry
  

http://www.umc.edu/Administration/Centers_and_Institutes/Center_for_Psychiatric_Neuroscience/Core_Research_Resources.aspx

Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core.

Proper citation: UMMC Center for Psychiatric Neuroscience Labs and Facilities (RRID:SCR_002688) Copy   

•   Source: SciCrunch Registry
  

http://projects.tcag.ca/lafora/

The Lafora database is a repository of information related to progressive myoclonus epilepsy mutation and polymorphism data. Users may view all mutations in the database(Mutations of EPM2A and NHLRC1(EPM2B)), click on individual exons for mutations, or search the database by keyword. Nucleotide and amino acids positions were assigned based on the GenBank reference sequence NM_005670 for EPM2A and NM_198586 for EPM2B. The data can be viewed using the XRT Table Browser, and where possible, links to external sources such as NCBI, PubMed are provided. At this time, the database is under development. The BioXRT (Cross-Referenced Tables) Table Browser is a highly configurable tool for viewing complex, table based information. The tables can be displayed using pre-set options, or customized to view arbitrary subsets of rows, columns or other features.

Proper citation: Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database (RRID:SCR_002919) Copy   

•   Source: SciCrunch Registry
  

http://www.atgc-montpellier.fr/

A bioinformatics platform that is a joint project of several South of France laboratories with available services based on their expertise, issued from their research activities which involve phylogenetics, population genetics, molecular evolution, genome dynamics, comparative and functional genomics, and transcriptome analysis. Most of the software and databases on ATGC are (co)authored by researchers from South of France teams. Some are widely used and highly cited. South of France laboratories: * CRBM (transcriptomes and stem cells). * IBC (computational biology). * MiVEGEC (evolution and phylogeny). * LGDP (plant genomics). * LIRMM (computer science). * South Green (plant genomics).

Proper citation: ATGC: Montpellier bioinformatics platform (RRID:SCR_002917) Copy   

•   Source: SciCrunch Registry
  

https://www.cu.edu/

University of Colorado is a four-campus system that includes the University of Colorado Boulder, the University of Colorado Colorado Springs, the University of Colorado Denver and the University of Colorado Anschutz Medical Campus.

Proper citation: University of Colorado; Colorado; USA (RRID:SCR_002910) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.nist.gov/hmpd/

Database of mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. The mitochondrion plays a central role in cellular metabolism, and evidence of mitochondrial involvement in a number of different human diseases is increasing. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases. Mitochondrial DNA Sequence: A graphical tool was developed to visualize the human mitochondrial DNA sequences that highlight coding regions for RNAs and proteins. Disease susceptible mutations are also noted in the sequence. Mitochondrial DNA Polymorphism: Human mitochondrial sequences of different ethnic groups were obtained from the Human Mitochondrial Genome Database. A DNA sequence analysis tool was developed to compare polymorphisms of different human mitochondrial DNA sequences. This tool allows the user to select mitochondrial sequences from any two human populations and compare them for sequences variations. Mitochondrial proteins related diseases: Malfunction of mitochondrial proteins affect many cells from brain, heart, liver, skeletal muscles, kidney, and the endocrine and the respiratory systems which lead to many diseases. Relevant information for mitochondrial related diseases from OMIM, the Neuromuscular Disease Center and MITOMAP are gathered, and mitochondrion-associated diseases are grouped, categorized, and linked to OMIM. 3-D Structures of Mitochondrial proteins: The available 3D structures for mitochondrial proteins are presented through a custom-made interface. A concise HTML page is generated for reporting the structural details and the associated information obtained from relevant web sites (PDBREPORT, Interatomic Contacts of Structural Units (CSU), PROCHECK, Ligand Protein Contacts (LPC), PROMOTIF and CastP). References are linked to the PubMed site. The 3-D structures are presented through the use of a Kinemage.

Proper citation: Human Mitochondrial Protein Database (RRID:SCR_002913) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/university-of-florida

Portal that lists and provides information on core facilities located at the University of Florida.

Proper citation: University of Florida Labs and Facilities (RRID:SCR_002912) Copy   

•   Source: SciCrunch Registry
  

http://hiv-web.lanl.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.

Proper citation: HIV Sequence Database (RRID:SCR_002906) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/Tools/msa/clustalw2/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

Proper citation: Clustal W2 (RRID:SCR_002909) Copy   

•   Source: SciCrunch Registry
  

http://pir.georgetown.edu/pro/

An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).

Proper citation: PRO (RRID:SCR_002902) Copy   

•   Source: SciCrunch Registry
  

https://www.writelatex.com

A collaboration tool which allows users to edit and publish scientific articles and papers. Overleaf utilizes the convenience of an easy-to-use WYSIWYG manuscript editor with real-time collaboration and structured, fully typeset output produced automatically. Authors can publish immediately and directly to their journal of choice while publishers can reduce their editorial and review turnaround times with powerful change tracking, commenting, and project lifecycle management features. It was formerly known as writeLaTex but changed its name to Overleaf in 2015.

Proper citation: Overleaf (RRID:SCR_003232) Copy   

•   Source: SciCrunch Registry
  

http://lalashan.mcmaster.ca/theobio/projects/index.php/WorkingWiki

Free software extension for MediaWiki that makes a wiki into an environment for collaborating on publication-quality manuscripts and software projects. It allows wiki users to work together on anything that can be done by using UNIX commands to transform textual source code into output. Researchers can use it to collaborate on programs written in R, python, C, or any other language, and there are special features to support easy work on LaTeX documents. It develops the potential of the wiki medium to serve as a combination collaborative text editor, development environment, revision control system, and publishing platform. Its potential uses are open-ended - its processing is controlled by makefiles that are straightforward to customize - and its modular design is intended to allow parts of it to be adapted to other purposes.

Proper citation: WorkingWiki (RRID:SCR_003231) Copy   

•   Source: SciCrunch Registry