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http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home

Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools.

Proper citation: Appion Package (RRID:SCR_016734) Copy   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Proper citation: ToppCluster (RRID:SCR_001503) Copy   

•   Source: SciCrunch Registry

https://github.com/macmanes-lab/BinPacker/blob/master/README

Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

Proper citation: BinPacker (RRID:SCR_017038) Copy   

•   Source: SciCrunch Registry

https://cab.spbu.ru/software/spades/

Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPAdes (RRID:SCR_000131) Copy   

•   Source: SciCrunch Registry

http://www.cnprc.ucdavis.edu/research/arc.aspx

The Analytical and Resource Core provides services and resources to the scientific research community in areas including hematology, clinical chemistry, genetics, immunology, endocrinology, flow cytometry, and pathogen detection. Available resources include biological specimens, viral stocks, DNA, and species-specific reagents. Scientists and staff associated with each of the seven Core Laboratories provide consultation in experimental design, sample collection, and data analysis, and offer assays that utilize species-specific reagents wherever possible. Core Laboratory scientists can also work with users to develop new assays to meet research needs. Training is available for all assays, and Core Laboratories equipment can be made available, typically on a recharge basis. Nonhuman primate resources developed at CNPRC are available to qualified individuals via the Resource Services component of the Core. * Clinical Laboratory * Endocrine Core Laboratory * Flow Cytometry Core Laboratory * Genetics Core Laboratory * Infectious Diseases Immunology Core Laboratory * Pathogen Detection Core Laboratory * Respiratory Disease Immunology Core Laboratory * Affiliated Laboratory: Clinical Proteomics Core Laboratory * Affiliated Laboratory: Microarray Core Facility * Resource Services: The following research resources of CNPRC are available to scientists on a recharge basis. ** Allergen: Characterized protein extracts of house dust mite (Dermatophagoides pteronyssinus and Dermatophagoides farinae) are available for allergen sensitization projects. ** Biological Specimens: Tissues collected at necropsy are available from rhesus monkeys (Macaca mulatta), cynomolgus monkeys (Macaca fascicularis), and titi monkeys (Callicebus cupreus). Contact: Biospecimens (at) primate.ucdavis.edu Blood samples are available through our blood donor program. ** Data: Data for colony animals are available from our computerized database. Data include birth records, weights, reproductive history, relocation history, etc. ** DNA: DNA extracted from peripheral blood mononuclear cells is available on animals of all age-sex classes from known pedigrees. ** Reagents and Samples: Reagents, controls, and known/unknown samples are available from the Pathogen Detection Core Laboratory. Samples include pedigreed sera/plasma, fixed tissues and DNA from macaques and various other species. Validated reagents for many pathogens are available, including SIV, SRV1-5, SFV, STLV, RRV, RhCMV, Herpes B, SV40, and LCV. More information is available at: http://pdl.primate.ucdavis.edu/PDLreagents.html. ** Shipping: Shipping services are available by trained staff who can properly document, package and ship critical experimental materials, including nonhuman primate samples. Assistance is also provided for obtaining CITES permits, required for international shipment of any nonhuman primate samples. ** Transformed B-Cell Lines: Cryopreserved Herpes papio - transformed B cell lines from over 300 rhesus monkeys in the CNPRC colony are available. Transformation of macaque B cells to establish a new cell line is available on request. ** Virus Stock: Rhesus Cytomegalovirus: A unique primary isolate, developed at CNPRC, is available. ** Virus Stock: Simian Immunodeficiency Virus: Aliquots of SIVmac251 and SIVmac239 virus stocks were prepared by propagation in peripheral blood mononuclear cells from rhesus macaques and contain approximately 100,000 50% tissue culture infectious doses per ml. As measured by the commercial SIV branched chain assay, SIVmac251 contains 2 x 109 copies of SIV RNA per ml and SIVmac239 contains 109 copies of SIV RNA per ml. These virus stocks are infectious for rhesus macaques by intravenous, intravaginal and oral routes of inoculation.

Proper citation: California National Primate Research Center Analytical and Resource Core (RRID:SCR_000696) Copy   

•   Source: SciCrunch Registry

http://icr.coh.org/

Group of 10 academic laboratories provide pancreatic islets of cGMP-quality to eligible investigators for use in FDA approved, IRB-approved transplantation protocols in which isolated human islets are transplanted into qualified patients afflicted with type 1 diabetes mellitus; optimize the harvest, purification, function, storage, and shipment of islets while developing tests that characterize the quality and predict the effectiveness of islets transplanted into patients with diabetes mellitus; and provide pancreatic islets for basic science studies. The centers are electronically linked through an Administrative and Bioinformatics Coordinating Center (ABCC). The ABCC manages a system with objectively defined criteria that establishes the order of priority for islet distribution. It also provides database and other informatics to track the utilization of pancreata and all distributed clinical grade islets for transplant and basic research, and supports the Islet Cell Resource Centers Consortium so that the research community has a single entry point to the program. Qualified researchers from domestic institutions may request islets by submitting a written application to the director of the ABCC. The ICRs will distribute Islets as appropriate for either clinical or basic science protocol use to eligible investigators who have received a favorable review and subsequent approval by the ICR Steering Committee (SC). The Administrative and Bioinformatics Coordinating Center (ABCC) manages the distribution according to a priority list. The ABCC will give preference to investigators who have peer-reviewed, NIH-funded research support.

Proper citation: Islet Cell Resource Centers (RRID:SCR_002806) Copy   

•   Source: SciCrunch Registry

http://ebirt.emory.edu/

Venue for research resource discovery offering resource providers a platform to advertise their services and products, as well as investigators a means to locate services for their use. Search results may be refined by resource type, research area or institution.

Proper citation: eBIRT (RRID:SCR_004172) Copy   

•   Source: SciCrunch Registry

http://www.genetrap.org/

Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy).

Proper citation: International Gene Trap Consortium (RRID:SCR_002305) Copy   

•   Source: SciCrunch Registry

https://cnprc.ucdavis.edu/

Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice.

Proper citation: California National Primate Research Center (RRID:SCR_006426) 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.loni.usc.edu/Software/LONI-Inspector

A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI.

Proper citation: LONI Inspector (RRID:SCR_004923) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/IO_Plugins

Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included.

Proper citation: LONI Java Image I/O Plugins (RRID:SCR_008277) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/retro/cobre.html

Data set of raw anatomical and functional MR data from 72 patients with Schizophrenia and 75 healthy controls (ages ranging from 18 to 65 in each group). All subjects were screened and excluded if they had: history of neurological disorder, history of mental retardation, history of severe head trauma with more than 5 minutes loss of consciousness, history of substance abuse or dependence within the last 12 months. Diagnostic information was collected using the Structured Clinical Interview used for DSM Disorders (SCID). A multi-echo MPRAGE (MEMPR) sequence was used with the following parameters: TR/TE/TI = 2530/(1.64, 3.5, 5.36, 7.22, 9.08)/900 ms, flip angle = 7��, FOV = 256x256 mm, Slab thickness = 176 mm, Matrix = 256x256x176, Voxel size =1x1x1 mm, Number of echos = 5, Pixel bandwidth =650 Hz, Total scan time = 6 min. With 5 echoes, the TR, TI and time to encode partitions for the MEMPR are similar to that of a conventional MPRAGE, resulting in similar GM/WM/CSF contrast. Rest data was collected with single-shot full k-space echo-planar imaging (EPI) with ramp sampling correction using the intercomissural line (AC-PC) as a reference (TR: 2 s, TE: 29 ms, matrix size: 64x64, 32 slices, voxel size: 3x3x4 mm3). Slice Acquisition Order: Rest scan - collected in the Axial plane - series ascending - multi slice mode - interleaved MPRAGE - collected in the Sag plane - series interleaved - multi slice mode - single shot The following data are released for every participant: * Resting fMRI * Anatomical MRI * Phenotypic data for every participant including: gender, age, handedness and diagnostic information.

Proper citation: COBRE (RRID:SCR_010482) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/genomics-core-facility-brown

Provides genomics and proteomics equipment to researchers at Brown University and to entire Rhode Island research community, as well as assistance with experimental design, trouble shooting, and data analysis. Offers Affymetrix microarray and Illumina NextGeneration services to academic community and external customers.

Proper citation: Brown University Genomics Core Facility (RRID:SCR_012217) Copy   

•   Source: SciCrunch Registry

https://www.k-inbre.org/pages/k-inbre_about_bio-core.html

The K-INBRE Bioinformatics Core collaborates with Kansas researchers to perform research on cell and developmental biology. Core aims to serve the needs of investigators engaged in computationally intensive biomedical research, and to promote education in bioinformatics to students and researchers across the state of Kansas.

Proper citation: Kansas State University - INBRE Bioinformatics Core Facility (RRID:SCR_012596) Copy   

•   Source: SciCrunch Registry

https://www.ngvbcc.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology.

Proper citation: National Gene Vector Biorepository (RRID:SCR_004760) Copy   

•   Source: SciCrunch Registry

https://bioams.llnl.gov/

Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers.

Proper citation: National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) Copy   

•   Source: SciCrunch Registry

http://www.preger.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods.

Proper citation: Primate Embryo Gene Expression Resource (RRID:SCR_002765) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/mouseportal/

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy   

•   Source: SciCrunch Registry

http://psf.cobre.ku.edu/cores/ppg/about

Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies.

Proper citation: Kansas University at Lawrence Protein Production Group Core Facility (RRID:SCR_017749) Copy   

•   Source: SciCrunch Registry