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http://cgsc.biology.yale.edu/index.php

The CGSC Collection contains only non-pathogenic BSL-1 laboratory strains, primarily genetic derivatives of Escherichia coli K-12, the laboratory strain widely used in genetic and molecular studies, but a few B strains. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer. The collection includes cultures of wild-type contributed from a number of laboratories and a few thousand derivatives carrying one or up to 29 mutations from among 3500 mutations in (or included in deletions spanning) more than 1300 different loci. Some combinations were constructed particularly for mapping purposes and are still used for teaching and for rapid localization, some for manifestation of a particular phenotype, some strains for transferring a particular region or for complementation analysis. Some plasmids, e.g., the Clarke and Carbon collection, F-primes, a number of toolkit plasmids, and a few classic plasmids are included, but it is not a comprehensive collection of plasmids. Additionally, we have recently acquired most of the strains from the Keio Collection of systematic individual gene knockout (deletion/kan insertion) strains.

Proper citation: CGSC (RRID:SCR_002303) Copy   

•   Source: SciCrunch Registry

http://cbl.uh.edu/ORION/research/software

ORION is our neuron reconstruction software package developed for the morphological reconstruction of neurons from confocal and multiphoton microscopy data. It accepts raw neuron stack data as input and it is capable of reconstructing the neuron structure, visualizing the output, and exporting the reconstruction in a variety of formats. We are developing tools that will enable Neuroscientists to explore single neuron function via sophisticated image analysis. Advanced optical imaging can produce both structural and functional data and is at the forefront of experimentally exploring the fast, small-scale dynamics of living neurons. Further, compartmental modeling of neuronal function enables rapid testing of hypotheses and estimating experimentally inaccessible parameters. Combining these two techniques will afford unprecedented capabilities in the study of single neuron function. Our software utility bridges the two Neuroscience techniques by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION Software (RRID:SCR_004389) Copy   

•   Source: SciCrunch Registry

http://www.inbre.montana.edu/bioinformatics/functional_genomics/index.html

Core provides instrumentation and support for academic investigators throughout Montana and Rocky Mountain west. For most instrumentation, facility provides instruction and supervision followed by independent user access. For those doing Affymetrix microarrays, facility can also accept RNA samples and provides full service processing. Assists with experimental planning and grantmanship phases.

Proper citation: Montana State University Functional Genomics Core Facility (RRID:SCR_009939) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://cloudreg.neurodata.io/

Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration.

Proper citation: CloudReg (RRID:SCR_022795) Copy   

•   Source: SciCrunch Registry

https://github.com/Kingsford-Group/kourami

Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.

Proper citation: Kourami (RRID:SCR_022280) Copy   

•   Source: SciCrunch Registry

https://isamplesorg.github.io/home/

Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications.

Proper citation: iSamples (RRID:SCR_021750) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Rascaf

Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data.

Proper citation: Rascaf (RRID:SCR_022014) Copy   

•   Source: SciCrunch Registry

https://plantcyc.org/content/plantcyc-15.2.0

Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

Proper citation: PlantCyc (RRID:SCR_002110) Copy   

•   Source: SciCrunch Registry

http://icatb.sourceforge.net/fusion/fusion_startup.php

A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1

Proper citation: Fusion ICA Toolbox (RRID:SCR_003494) Copy   

•   Source: SciCrunch Registry

http://ccr.coriell.org/Sections/Collections/IPBIR/?SsId=18

The purpose of the IPBIR - Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics. Further research in these areas will advance our understanding of human origins, the biological basis of cognitive processes, evolutionary history and relationships, and social structure, and will provide critical scientific information needed to facilitate conservation of biological diversity. The derived DNA will be openly available to the broad scientific community who agree to restrict use to non-commercial purposes. DNA and cell culture samples are distributed only to qualified professional persons who are associated with recognized research, medical, or educational organizations engaged in research.

Proper citation: IPBIR - Integrated Primate Biomaterials and Information Resource (RRID:SCR_004614) Copy   

•   Source: SciCrunch Registry

http://datalad.org/

Project to adapt model of open source software distributions to address technical limitations of data sharing and develop all components of data distribution. Builds on top of git-annex and extends it with intuitive command line interface. Enables users to operate on data using familiar concepts, such as files and directories, while transparently managing data access and authorization with underlying hosting providers. Can create DataLad datasets using any data files published on the web.

Proper citation: DataLad (RRID:SCR_003931) Copy   

•   Source: SciCrunch Registry

http://www.delsaglobal.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 1, 2022. Organization whose mission is to build and promote a sustainable ecosystem of professional societies, funding agencies, foundations, companies, and citizens together with life science researchers and innovators in computing, infrastructure and analysis with the expressed goal of translating new discoveries into tools, resources and products.

Proper citation: DELSA (RRID:SCR_006231) Copy   

•   Source: SciCrunch Registry

https://www.msu.edu/~brains/brains/human/index.html

A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp

Proper citation: Human Brain Atlas (RRID:SCR_006131) Copy   

•   Source: SciCrunch Registry

https://www.xsede.org/

XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools.

Proper citation: XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) Copy   

•   Source: SciCrunch Registry

http://www.autopack.org/

A specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA.

Proper citation: Cellpack (RRID:SCR_006831) Copy   

•   Source: SciCrunch Registry

http://www.nsgportal.org/

Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists.

Proper citation: Neuroscience Gateway (RRID:SCR_008915) Copy   

•   Source: SciCrunch Registry

http://tulane.edu/som/regenmed/services/index.cfm

The Stem Cell Research and Regenerative Medicine''s Tissue Culture Core provides cells for research use within the department, as well as for distribution to other facilities. The core obtains hMSCs from bone marrow donor samples and expands these cells for research use. The hMSC''s are also characterized for bone, fat and cartilage differentiation, and are stored on site for use. The Tissue Culture Core also handles the expansion and characterization of mouse and rat MSC''s. The animal cells are cultured in a separate area, and never interact with human derived cells. We also have a supply of hMSC''s marked with GFP+, Mito Red and Mito Blue available.

Proper citation: Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core (RRID:SCR_007342) Copy   

•   Source: SciCrunch Registry

https://dna.dbi.udel.edu/

Provides genomics and molecular biology services for University of Delaware research groups and outside users.Supports genomic research through established expertise with genomics technologies.

Proper citation: University of Delaware Sequencing and Genotyping Center Core Facility (RRID:SCR_012230) Copy   

•   Source: SciCrunch Registry