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http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html#

A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU)

Proper citation: ADHD-200 Sample (RRID:SCR_005358) Copy   

•   Source: SciCrunch Registry

http://cbrain.mcgill.ca/

A flexible software platform for distributed processing, analysis, exchange and visualization of brain imaging data. The expected result is a middleware platform that will render the processing environment (hardware, operating systems, storage servers, etc...) transparent to a remote user. Interaction with a standard web browser allows application of complex algorithm pipelines to large datasets stored at remote locations using a mixture of network available resources such as small clusters, neuroimaging tools and databases as well as Compute Canada's High Performance Computing Centers (HPC). Though the focus of CBRAIN is providing tools for use by brain imaging researchers, the platform is generalizable to other imaging domains, such as radiology, surgical planning and heart imaging, with profound consequences for Canadian medical research. CBRAIN expanded its concept to include international partners in the US, Germany and Korea. As of December 2010, GBRAIN has made significant progress with the original three partners and has developed new partners in Singapore, China, India, and Latin America. CBRAIN is currently deployed on 6 Compute Canada HPC clusters, one German HPC cluster and 3 clusters local to McGill University Campus, totaling more than 80,000 potential CPU cores.

Proper citation: CBRAIN (RRID:SCR_005513) Copy   

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https://www.psych.udel.edu/graduate/areas-of-study/behavioral-neuroscience/nature-and-goals-of-the-program

Ph.D. program in Behavioral Neuroscience is committed to training exceptional students for independent neuroscience research careers in academic, governmental, or industrial settings. Our program provides training in biological foundations of behavior, with particular focus on sensation, learning and memory, affect, development, and neural plasticity.

Proper citation: University of Delaware Behavioral Neuroscience Graduate Program (RRID:SCR_005353) Copy   

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http://primegens.org/

A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing.

Proper citation: PRIMEGENS (RRID:SCR_005474) Copy   

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http://bowtie-bio.sourceforge.net/index.shtml

Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.

Proper citation: Bowtie (RRID:SCR_005476) Copy   

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http://www.labman.org

On March 8, 2008 in Havana, the Latin American Network for Brain Mapping (LABMAN) was created with participants from Argentina, Brazil, Colombia, Cuba and Mexico. The focus of LABMAN is to promote neuroimaging and systems neuroscience in the region through the implementation of training and exchange programs, and to increase public awareness of the Latin American potential to contribute both to basic and applied research in human brain mapping. The immediate LABMAN goals are to: * Train specialists in all major imaging techniques. * Expedite the transfer of new scientific and technical knowledge from abroad. * Increase the scientific productivity of the region. * Drastically increase the awareness of local governments, international organizations and of the general public of brain mapping results on potential. * Organize multinational projects in areas of special relevance to the region, e.g. nutrition, pediatric development, neurodegeneration. Latin American Brain Mapping Network (LABMAN) participants : * Cuban Neuroscience Center * University of Buenos Aires * University of Sao Paulo * Universidad del Valle, Cal��, Colombia * UAM Iztapalapa, Mexico City, Mexico

Proper citation: Latin American Brain Mapping Network (LABMAN) (RRID:SCR_005509) Copy   

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http://www.esourceresearch.org/

Inside e-Source you will find 20 interactive chapters with authoritative answers to methodological questions on behavioral and social science research. With contributions from a team of international experts, this anthology provides the latest information on addressing emerging challenges in public health. Book contents include: Setting the Scene, Describing How, Explaining Why, What Works, Emerging Issues. Tables, Figures, Exercises and Examples are included. Login for enhanced functionality. Contents: * Appropriate Research Methods * ''Science'' in the Social Sciences * Design Decisions in Research * Theory Development * Social and Behavioral Theories * Sample Surveys * Social Survey Data Collection * Administrative Data Systems * Observational Studies * Qualitative Methods * Conversation Analysis * Software and Qualitative Analysis * Clinical Trials * Cluster Unit Randomized Trials * Ethical Challenges * Multilevel Modeling * Objective Measurement of Subjective Phenomena * Measuring Socioeconomic Status * Evaluating the Quality of Health Care * Patient-Reported Outcomes

Proper citation: e-Source: Behavioral and Social Sciences Research (RRID:SCR_005627) Copy   

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http://microbesonline.org/

MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

Proper citation: MicrobesOnline (RRID:SCR_005507) Copy   

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http://grants.nih.gov/podcasts/All_About_Grants/index.htm

The Office of Extramural Research (OER) presents conversations with NIH staff members. Designed for investigators, fellows, students, research administrators, and others, we provide insights on grant topics from those who live and breathe the information. In mp3 and updated monthly. Transcripts are also available. So You Wanna... Keep Up with What''''s Hot? Prepare a Successful Grant Application? Suggest a Topic? Understand How Your Grant is Reviewed? Be an NIH Investigator?

Proper citation: All About Grants Podcast (RRID:SCR_005621) Copy   

•   Source: SciCrunch Registry

http://www.hca-vision.com/product_spot.html

Software package for analysis of microarray images. Microarray spot detection and characterization software package which extracts numerical information from cDNA microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPOT (RRID:SCR_005623) Copy   

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http://slicer.org/

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

Proper citation: 3D Slicer (RRID:SCR_005619) Copy   

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http://brainstars.org

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API.

Proper citation: BrainStars (RRID:SCR_005810) Copy   

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http://www.garban.org/garban/home.php

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool

Proper citation: GARBAN (RRID:SCR_005778) Copy   

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http://corneliu.henegar.info/FunCluster.htm

FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed clustering procedure involving biological annotations and gene expression data. FunCluster''''s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo Sapiens, Mus Musculus and Saccharomyces Cerevisiae. FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix). Download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: FunCluster (RRID:SCR_005774) Copy   

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http://vibez.informatik.uni-freiburg.de/

An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1����m^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download. ViBE-Z provides a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern. The ViBE-Z database, atlas and software are provided via a web interface.

Proper citation: ViBE-Z (RRID:SCR_005895) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/ws/ws.php?entry=BLASTatlas

The BLASTatlas is a tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms using either blastp, blastn, tblastn, or blastx. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots. The tool is SOAP compliant and WSDL (web services description language) files are available with programming examples available in Perl. The resolution is per-residue or per nucleotide depending on the regime of the blast search: For each annotation in the reference genome, the best hit in the database genome is found using one of the above algorithms. Each matching or mismatching residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the genome sequence, using the coordinates provided in the annotations. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set.

Proper citation: BLASTatlas - Mapping of whole genome homology (RRID:SCR_005891) Copy   

•   Source: SciCrunch Registry

https://fairsharing.org/standards/

Catalogue to: 1, centralize community-developed bioscience standards, linking to policies, other portals, open access resources and lists of tools and databases implementing the standards; 2. develop and maintain a set of criteria for assessing the usability and popularity of the standards, also the interoperability and relations among them; 3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems. Research community, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated. Similar trends in both the regulatory arena and commercial science. The BioSharing catalogue classifies standards into three types: * reporting requirements (minimal information checklists to report of the same core set of information) * terminological artifacts (such as controlled vocabularies and ontologies to describe the information) * exchange formats (to communicate the information) You can sort columns and browse the reporting guidelines content, or you can view all the standards, or reporting guidelines, or terminological artifacts or exchange formats only. Contribute and help build the catalogue.

Proper citation: FAIRSharing Catalogue of Standards (RRID:SCR_005926) Copy   

•   Source: SciCrunch Registry

http://great.stanford.edu/public/html/splash.php

Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool

Proper citation: GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) Copy   

•   Source: SciCrunch Registry

http://www.curehunter.com/public/showTopPage.do

CureHunter is the only fully integrated scientific search, data retrieval and analysis engine on the web that can read the entire US National Library of Medicine Medline Archive and automatically extract and quantify the evidence for successful clinical outcomes of all known drugs for all known human diseases. * For patients we provide low-cost Summary PDF Reports with all drug evidence for all known cures or symptom improvement * For medical professionals CureHunter on-line access delivers decision support in 10-20 seconds of real clinical time to make an evidence check as SOP as a BP or Temp * For pharma research scientists we offer powerful data export functions that deliver over 1.5 million specific clinical outcome data points to new drug discovery software Use the CureHunter Research Interface: * Discover new potential off-label applications * Export data and apply custom analytics * 1-click drug performance meta-analyses * Keep up-to-date on the latest developments in your field * Optimize formularies with total evidence-based objectivity * RSS Feeds for Tracking Pharma Products

Proper citation: CureHunter (RRID:SCR_005804) Copy   

•   Source: SciCrunch Registry

http://www.hormone.org/

A portal for hormone-related health information for the public, physicians, allied health professionals and the media. It serves as a resource for the public by promoting the prevention, treatment and cure of hormone-related conditions through outreach and education. It provides free educational materials, public forums, physician referral service, and media education campaigns. It offers a library of educational materials and programs covering a wide range of endocrine topics, including adrenal disorders, breast cancer, diabetes, osteoporosis, stress, thyroid disease and cancer.

Proper citation: Hormone Health Network (RRID:SCR_005765) Copy   

•   Source: SciCrunch Registry