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http://pivotcollections.org/collection.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. Mouse brains displayed in the Microsoft Silverlight PivotViewer from the Mouse Brain Library (MBL) which consist of high-resolution images of brains from many genetically characterized strains of mice. PivotViewer makes it easier to interact with massive amounts of data on the web in ways that are powerful, informative, and fun. By visualizing thousands of related items at once, users can see trends and patterns that would be hidden when looking at one item at a time. Because PivotViewer leverages Deep Zoom, it displays full, high-resolution content without long load times, while the animations and natural transitions provide context and prevent users from feeling overwhelmed by large quantities of information. This simple, inviting interaction model encourages exploration and longer audience engagement times, and applies broadly to a variety of content types.

Proper citation: MBL Pivot Collection (RRID:SCR_005506) Copy   

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http://snap.cs.berkeley.edu/

A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

Proper citation: Scalable Nucleotide Alignment Program (RRID:SCR_005501) Copy   

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http://mta.hu/english/

The Hungarian Academy of Sciences is the most important and prestigious learned society of Hungary. Its seat is at the bank of the Danube in Budapest, between Széchenyi rakpart and Akadémia utca.

Proper citation: Hungarian Academy of Sciences; Budapest; Hungary (RRID:SCR_005654) Copy   

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http://neuromorphometrics.com

Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas.

Proper citation: Neuromorphometrics (RRID:SCR_005656) Copy   

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http://www.phrap.org/consed/consed.html

A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Proper citation: Consed (RRID:SCR_005650) Copy   

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http://www.xuvtools.org/

XuvTools (pronounced ex-you-vee-tools) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). The goal of XuvTools is to provide tools, that combine multiple microscopic recordings to obtain a larger field of view (stitching) and a higher dynamic range (HDR recombination), or better resolution (multi view reconstruction), and to make these tools publicly available. What XuvTools can do: * Full 3D Stitching * Scaling, if the voxel sizes are known from image data * Fully automatic stitching modes * Manual pre-alignment modes * Arbitrary large datasets * Reads stage coordinates if available * free, no hidden costs * Reads many many input formats via LOCI Bio-Formats and Dmitry Fedorov''s BioImage. Limitations of XuvTools: (current limitations, we are working on it!) * No 2D Stitching: stacks need 4 Z-slices or more * No memory management: You need lots of RAM * No rotational alignment * The only supported output formats are: Imaris, HDF5 (No TIFF output support)

Proper citation: XuvTools (RRID:SCR_005894) Copy   

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http://basalganglia.huji.ac.il/links.htm

GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GOdist (RRID:SCR_005770) Copy   

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http://caps.ucsf.edu/

Established in 1986, the Center for AIDS Prevention Studies (CAPS) at the University California, San Francisco (UCSF) is the world''s largest research center dedicated to social, behavioral, and policy science approaches to HIV. The mission of the CAPS is to conduct research to prevent new HIV infections, improve health outcomes among those infected, and reduce disparities. This is how we do it: * CAPS provides core support for multidisciplinary and high-impact HIV research, enhances the excellence of research projects, trains a new generation of HIV scientists, and assists implementing partners. * Our Administrative Core provides strong leadership and management to stimulate innovative research and ensure scientific rigor and sound fiscal operations. * Our Developmental Core fosters innovative, high-impact, multidisciplinary HIV research by providing funds for innovative pilot work, sponsoring training and education, and ensuring the scientific excellence of research. * Our Methods Core provides comprehensive methodological training and consultation in research design, qualitative and quantitative analysis, and state-of-the-art data collection and management. * Our Policy and Ethics Core stimulates and supports policy-relevant research, identifies and analyzes the policy and ethics implications of research, and ensures the highest ethical conduct of research. * Our Technology and Information Exchange (Domestic Response) Core responds to the domestic epidemic by disseminating information, fostering community collaborative research, providing technical assistance and capacity-building to community-based organizations, and learning from community expertise. * Our Global Response Core responds to the global epidemic by fostering collaborative research with scientists in developing countries, completing and disseminating Cochrane Collaborative scientific reviews, and providing technical assistance, capacity building, and an evidence base to implementing partners.

Proper citation: UCSF Center for AIDS Prevention Studies (CAPS) (RRID:SCR_005647) Copy   

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http://zfin.org/zf_info/anatomy/dict/sum.html

A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability.

Proper citation: Zebrafish Anatomical Ontology (RRID:SCR_005887) Copy   

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http://www.unr.edu/

Public land-grant research university in Reno, Nevada.

Proper citation: University of Nevada at Reno; Nevada; USA (RRID:SCR_005882) Copy   

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http://edwardslab.bmcb.georgetown.edu/ws/peptideMapper/

The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter.

Proper citation: PeptideMapper (RRID:SCR_005763) Copy   

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http://www.nature.com/nrg/journal/v3/n2/box/nrg728_BX2.html

This file describes a selection of the behavioral paradigms that have been useful in behaviorally phenotyping mouse mutants.

Proper citation: The Mouse: Genetics meets Behavior (RRID:SCR_005884) Copy   

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http://www.chemnavigator.com/cnc/services/SCSORS_Overview.asp

ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years.

Proper citation: SCSORS - Semi-Custom Synthesis On-line Request System (RRID:SCR_005636) Copy   

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http://ngsview.sourceforge.net/

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

Proper citation: NGSView (RRID:SCR_005637) Copy   

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http://www.topsan.org/

Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation.

Proper citation: TOPSAN (RRID:SCR_005758) Copy   

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https://code.google.com/p/pepr-chip-seq/

A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.

Proper citation: PePr (RRID:SCR_005759) Copy   

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http://cgap.nci.nih.gov/Genes/GOBrowser

With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool

Proper citation: CGAP GO Browser (RRID:SCR_005676) Copy   

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http://vortex.cs.wayne.edu/projects.htm#Onto-Express

The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool

Proper citation: Onto-Express (RRID:SCR_005670) Copy   

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http://www.genmapp.org/help_v2/UsingMAPPFinder.htm

MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible

Proper citation: MAPPFinder (RRID:SCR_005791) Copy   

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https://code.google.com/p/bsmap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Short reads mapping software for bisulfite sequencing reads.

Proper citation: BSMAP (RRID:SCR_005671) Copy   

•   Source: SciCrunch Registry