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http://www.stanford.edu/group/brainsinsilicon/neurogrid.html
A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices.
Proper citation: Neurogrid (RRID:SCR_005024) Copy
Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.
Proper citation: SMART (RRID:SCR_005026) Copy
An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.
Proper citation: UPARSE (RRID:SCR_005020) Copy
http://birdgenenames.org/cgnc/
International group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups.
Proper citation: Chicken Gene Nomenclature Consortium (RRID:SCR_004966) Copy
An Antibody supplier, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BioVision (RRID:SCR_005057) Copy
http://www.keralauniversity.ac.in/
University of Kerala, formerly the University of Travancore, is an affiliating university located in Thiruvananthapuram, capital of the state of Kerala, India.
Proper citation: University of Kerala; Kerala; India (RRID:SCR_005059) Copy
http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/47-carma?highlight=WyJjYXJtYSJd
A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system.
Proper citation: CARMA (RRID:SCR_004999) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.
Proper citation: SMD (RRID:SCR_004987) Copy
http://mitcr.milaboratory.com/
An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data.
Proper citation: MiTCR (RRID:SCR_004989) Copy
http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/
A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.
Proper citation: MIP Scaffolder (RRID:SCR_005072) Copy
http://compbio.cs.toronto.edu/hapsembler/scarpa.html
A stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data.
Proper citation: Scarpa (RRID:SCR_005073) Copy
http://neuroscienceblueprint.nih.gov/factSheet/MicronCon.htm
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis.
Proper citation: NIH Neuroscience Microarray Consortium (RRID:SCR_004930) Copy
http://www.bmbf.de/en/index.php
Proper citation: German Federal Ministry of Education and Research (RRID:SCR_005066) Copy
The Alzheimer's and Dementia Resource Center (ADRC) facilitates tissue donations for the Brain Bank Research Program in order to help find better treatments, more diagnostic tools and a cure for Alzheimer's disease and dementia. The Brain Bank Program is administered by Mount Sinai Medical Center in Miami Beach and under contract with the Florida Department of Elder Affairs. ADRC also provides caregivers with the educational resources, spiritual comfort and emotional support. The ADRC facilitates training for professional caregivers that meets requirements for the Florida Department of Elder Affairs.
Proper citation: Alzheimer's and Dementia Resource Center (RRID:SCR_004924) Copy
http://purl.bioontology.org/ontology/PHENOMEBLAST
A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases.
Proper citation: PhenomeBLAST Ontology (RRID:SCR_005139) Copy
http://petrov.stanford.edu/cgi-bin/Tlex.html
Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data.
Proper citation: T-lex (RRID:SCR_005134) Copy
https://code.google.com/p/popoolationte/
A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file).
Proper citation: PoPoolation TE (RRID:SCR_005131) Copy
The Alfred P. Sloan Foundation is a philanthropic, not-for-profit grantmaking institution based in New York City. Established in 1934 by Alfred Pritchard Sloan Jr., then-President and Chief Executive Officer of the General Motors Corporation, the Foundation makes grants in support of original research and education in science, technology, engineering, mathematics and economic performance. * Promotes research in science, technology, engineering, mathematics, and economic performance * Offers two-year long research fellowships for early career researchers
Proper citation: Alfred P. Sloan Foundation (RRID:SCR_005099) Copy
https://datashare.ed.ac.uk/handle/10283/3844
Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays.
Proper citation: Eurexpress (RRID:SCR_005093) Copy
A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl.
Proper citation: BEERS (RRID:SCR_005090) Copy
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