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https://www.fitzgerald-fii.com

Commercial organization that supplies antibodies, proteins, ELISA kits, serum, and plasma to the research community.

Proper citation: Fitzgerald Industries International (RRID:SCR_003237) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/bctnet/datasets

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. This site has a collection of cortical connectivity datasets and modeling software components that can be downloaded and used for modeling of cortical circuits. The toolbox combines Matlab functions and neuroanatomical data sets useful in the analysis of structural or functional brain networks. Several people have made contributions and if you wish to contribute yourself with a new function or set of functions please contact osporns_at_indiana.edu.The following is a collection of commonly used large scale cortical connectivity data sets compiled from tract-tracing studies. Hence nodes represent cortical areas and links represent large cortico-cortical tracts. * macaque71.mat (BD network). Macaque cortical connectivity: 71 nodes 746 links. Reference: Young (1993). Contributor: OS. Used in e.g. Sporns (2002). * fve30.mat; fve32.mat (BD networks). Two version the macaque visual cortex. fve30.mat: 30 nodes 311 links. fve32.mat: 32 nodes 320 links. Reference: Felleman and van Essen (1991). Contributor: OS. Used in e.g. Sportns et al. (2000) Sporns and Kotter (2004). * macaque47.mat (BD network). Large scale cortico-cortical connectivity matrix of the visual and sensorimotor areas in the macaque. 47 nodes; 505 links. Used in e.g. Honey et al. (2007). Contributor: RK. * cat.mat (WD networks). Connection matrices of cat cortex. CIJall contains all cortical and thalamic areas: 95 nodes 2126 links. CIJctx contains only 52 cortical areas: 52 nodes 820 links. Reference: Scannell et al. (1999). Contributor: OS. Used in e.g. Sporns and Zwi (2004) Sporns and Kotter (2004). * DSIhumanctx.mat (WU networks).

Proper citation: Cortical connectivity data sets (RRID:SCR_003190) Copy   

•   Source: SciCrunch Registry

https://www.assays.co.il

Commercial organization that provides services for assay development, research histopathology, and early stage project consultation.

Proper citation: Smart Assays (RRID:SCR_003195) Copy   

•   Source: SciCrunch Registry

http://www.mged.org/mage-tab/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.

Proper citation: MAGE-TAB (RRID:SCR_003222) Copy   

•   Source: SciCrunch Registry

http://www.fged.org/projects/minseqe/

The Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guidelines for microarray experiments, adherence to the MINSEQE guidelines will improve integration of multiple experiments across different modalities, thereby maximising the value of high-throughput research. The five elements of experimental description considered essential when making data available supporting published high-throughput sequencing experiments are as follows: # The description of the biological system, samples, and the experimental variables being studied # The sequence read data for each assay # The "final" processed (or summary) data for the set of assays in the study # General information about the experiment and sample-data relationships # Essential experimental and data processing protocols

Proper citation: MINSEQE (RRID:SCR_003221) Copy   

•   Source: SciCrunch Registry

http://146.20.110.164/about/

Tools for researchers to connect their data, code and computational methods to their published or soon to be published research in a convenient and easily citeable form. ResearchCompendia provides the tools to publish digital scholarly objects by hosting data, code, and methods in a form that is accessible, trackable, and persistent. They provide hosting and computational cloud resources for all researchers. Data and code should be citable and linked to the original publication.

Proper citation: ResearchCompendia (RRID:SCR_003223) Copy   

•   Source: SciCrunch Registry

http://creskolab.uoregon.edu/stacks/

A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Proper citation: Stacks (RRID:SCR_003184) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/dbvar/

Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.

Proper citation: dbVar (RRID:SCR_003219) Copy   

•   Source: SciCrunch Registry

https://neurobiobank.nih.gov/

National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor.

Proper citation: NIH NeuroBioBank (RRID:SCR_003131) Copy   

•   Source: SciCrunch Registry

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

Proper citation: RNAhybrid (RRID:SCR_003252) Copy   

•   Source: SciCrunch Registry

http://cal.tongji.edu.cn/PlantLoc/index.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.

Proper citation: PlantLoc (RRID:SCR_003138) Copy   

•   Source: SciCrunch Registry

http://www.stereologyresourcecenter.com/

A company of professionally trained stereologists, bioscientists, computer engineers, educators, and support personnel that provides comprehensive neurostereology products and services to the global bioscience community. These products and services include: stereology and image analysis software, digital imaging technology, turnkey stereologer solutions, comprehensive stereology and image analysis/image processing software, professional contract services, neurostereology workshops, basic stereology courses, and online stereology webinars. The Center also offers tissue processing (sectioning, staining, slide preparation) and stereology data collection services. Researchers may use equipment and facilities to complete projects with full confidentiality and according to Good Laboratory Practices guidelines.

Proper citation: Stereology Resource Center (RRID:SCR_003137) Copy   

•   Source: SciCrunch Registry

http://www.uccs.edu/

Public university that offers degrees in the social sciences, humanities, and natural sciences.

Proper citation: University of Colorado; Colorado Springs; USA (RRID:SCR_003130) Copy   

•   Source: SciCrunch Registry

http://www.brc.riken.jp/inf/en

RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad.

Proper citation: RIKEN BioResource Center (RRID:SCR_003250) Copy   

•   Source: SciCrunch Registry

http://mrsfast.sourceforge.net/

A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)

Proper citation: mrsFAST (RRID:SCR_003128) Copy   

•   Source: SciCrunch Registry

http://talkbank.org/

Databases of transcript and media data collected from conversations with adults and older children to foster fundamental research in the study of human and animal communication. Conversations with children are available from CHILDES. All of the data is transcribed in CHAT and CA/CHAT formats. Databases of the following types are included in the collection: Aphasia patient speech, Child speech, Study of Phonological Development, Conversation Analysis, and Bilingualism and Second Language Acquisition. TalkBank will use these databases to advance the development of standards and tools for creating, sharing, searching, and commenting upon primary materials via networked computers.

Proper citation: TalkBank (RRID:SCR_003242) Copy   

•   Source: SciCrunch Registry

http://acgt.cs.tau.ac.il/hyden/

Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).

Proper citation: HYDEN (RRID:SCR_003126) Copy   

•   Source: SciCrunch Registry

http://nmrml.org/cv/

Ontology for describing NMR experiments and acquisitions.

Proper citation: nmrCV (RRID:SCR_003247) Copy   

•   Source: SciCrunch Registry

http://www.metabolomics-msi.org

Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations.

Proper citation: Metabolomics Standards Initiative (RRID:SCR_003246) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/burgelab/miso/

Probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq and identifies differentially regulated isoforms or exons across samples.

Proper citation: MISO (RRID:SCR_003124) Copy   

•   Source: SciCrunch Registry