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http://www.catapultgenetics.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 31, 2022. Data services to support validation of economically relevant traits for the livestock industries. Sponsors: This resource is supported by Pfizer Animal Health. Keywords: Animal, Genetics, Health, World, Genetic, Information, Service, Industry, Livestock, DNA, Maker, Technology, Phenotypic, Productivity,

Proper citation: Pfizer Animal Genetics (RRID:SCR_008447) Copy   

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http://www.broad.mit.edu/cancer/software/genecluster2/gc2.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding supervised classification, gene selection, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbor (KNN) algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. It enhances the clustering capabilities of GeneCluster 1.0 by adding a module for batch SOM clustering, and also includes a marker gene finder based on a KNN analysis and a visualization module. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater.

Proper citation: GeneCluster 2: An Advanced Toolset for Bioarray Analysis (RRID:SCR_008446) Copy   

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http://www.emdbiosciences.com

A commercial antibody company.

Proper citation: EMD4Biosciences (RRID:SCR_008441) Copy   

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http://predictioncenter.org/casp7/Casp7.html

The main goal of CASP is to obtain an in-depth and objective assessment of our current abilities and inabilities in the area of protein structure prediction. To this end, participants will predict as much as possible about a set of soon to be known structures. These will be true predictions, not ''post-dictions'' made on already known structures. Sponsors: This resource is supported by the US National Library of Medicine (NIH/NLM), National Institute of General Medical Sciences (NIH/NIGMS), BioSapiens Network of Excellence, and HP Invent. Keywords: Clinical, Technique, Protein, Prediction, Structure,

Proper citation: Critical Assessment of Techniques for Protein Structure Prediction (RRID:SCR_008434) Copy   

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http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT

Proper citation: Vienna RNA (RRID:SCR_008550) Copy   

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http://www.loci.wisc.edu/home/

LOCI is a biophotonics instrumentation laboratory stemming from the research activities of Kevin Eliceiri, Dave Beebe, Bill Bement, Paul Campagnola, Patti Keely, Brenda Ogle, Justin Williams and other LOCI investigators. Our mission is to develop advanced optical and computational techniques for imaging and experimentally manipulating living specimens. New and improved imaging instrumentation and optical-based experimental techniques are being developed. These projects are driven by demands arising from the scientific studies of external collaborators and the principal investigators and opportunities that arise with the emergence of new technology. Instrumentation development is undertaken in a form that is both accessible and beneficial to the scientific community. LOCI is directed by Kevin Eliceiri, and all inquiries about LOCI collaborations or general imaging questions may be directed to him.

Proper citation: LOCI (RRID:SCR_008552) Copy   

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http://www.who.int/en/

The directing and coordinating authority responsible for public health within the United Nations system. The WHO Regional Office for Europe (WHO/Europe) is one of the six regional offices around the world. It serves the WHO European Region, which comprises 53 countries from the Atlantic to the Pacific oceans. WHO/Europe collaborates with a range of public health stakeholders in the Region and globally, to ensure that coordinated action is taken to develop and implement efficient health policies and to strengthen health systems. WHO/Europe is made up of public health, scientific, and technical experts.

Proper citation: World Health Organization (RRID:SCR_008505) Copy   

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http://kyotofly.kit.jp/cgi-bin/stocks/data_search.cgi

Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request.

Proper citation: Kyoto Stock Center (RRID:SCR_008469) Copy   

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http://www.genome.ou.edu/cneo.html

Cryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet.

Proper citation: Cryptococcus Neoformans cDNA Sequencing (RRID:SCR_008462) Copy   

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http://cosyne.org

The annual Cosyne meeting provides an inclusive forum for the exchange of experimental and theoretical/computational approaches to problems in systems neuroscience. The first Cosyne meeting, held in 2004 at Cold Spring Harbor Laboratory, drew over 350 participants. Since 2005, the meeting has been held in Salt Lake City, Utah. It has attracted a growing number of participants, from nearly 400 in 2005 to over 500 in 2010. To encourage interdisciplinary interactions, the main meeting is arranged in a single track. A set of invited talks are selected by the Executive Committee, and additional talks and posters are selected by the Program Committee, based on submitted abstracts. Cosyne topics include but are not limited to: neural coding, natural scene statistics, dendritic computation, neural basis of persistent activity, nonlinear receptive field mapping, representations of time and sequence, reward systems, decision-making, synaptic plasticity, map formation and plasticity, population coding, attention, computation with spiking networks. Sponsor. Thanks to the generosity of The Gatsby Charitable Foundation, of Qualcomm Incorporated and of Brain Corporation, up to 40 travel grants will be available to support student and postdoc participation in the main Cosyne meeting.

Proper citation: Computational and Systems Neuroscience 2011 (RRID:SCR_008459) Copy   

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http://bio.informatics.iupui.edu/cmaps

C-Maps project is an international collaboration between Discovery Informatics and Computing Laboratory in Indiana University Purdue University Indianapolis (IUPUI) and State Key Laboratory of Intelligent Technology and Systems (LITS) in Tsinghua University China. Connectivity Maps (C-Maps) is created to connect diseases with genes/proteins whose mutations cause them and drugs which treat them. Recent studies focus on developing systematic methods to build C-Maps using gene-expression data to connect small molecules, genes, and disease. Justin Lamb et. al. established a systematic approach to build C-Map using gene-expression profiling as the common vocabulary to connect small molecules, genes, and diseases. They created the first installment of a reference collection of gene-expression profiles from cultured human cell treated with bioactive small molecules, together with pattern-matching software to mine these data [1]. Atul J Butte et. al build a C-Maps using the UMLS (Unified Medical Language System) annotation of gene expression data to connect phenotypic, disease, environmental and experimental contexts as well as genes with differential expression associated with these concepts [2] Sponsor. We would like to thank the generous grant support from Indiana University - Purdue University Indianapolis, and National Basic Research Program of China (973 Program), National High Technology Research and Development Program of China (863 Program).

Proper citation: Connectivity Maps Web Services (RRID:SCR_008453) Copy   

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http://www.alivelearn.net/xjview8/

A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).

Proper citation: xjView: A Viewing Program For SPM (RRID:SCR_008642) Copy   

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http://bdtnp.lbl.gov/Fly-Net/index.jsp?w=home

The goal of this project is to decipher the transcriptional information contained in the extensive cis-acting DNA sequences that direct the patterns of gene expression that underlie animal development. Using the early embryo of the fruitfly Drosophila melanogaster as a model, these researchers are developing experimental and computational methods to systematically characterize and dissect the complex expression patterns and regulatory interactions already present prior to gastrulation. They have identified 37 principal regulatory factors within this network for initial analysis together with their target genes. Sponsors: This project is chiefly funded by a grant from NIGMS and NHGRI, R01 GM070444. Additional funding comes from grants to Michael Eisen, Sue Celniker, and Bernd Hamann.

Proper citation: Berkeley Drosophila Transcription Network Project (RRID:SCR_008640) Copy   

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http://lowelab.ucsc.edu/tRNAscan-SE

Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).

Proper citation: tRNAscan-SE (RRID:SCR_008637) Copy   

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http://neuroprosight.scs.uiuc.edu/

NeuroProSight allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using the Top-Down Approach. This site has many tools and graphical features to facilitate analysis of single (recombinant) proteins, proteins in mixtures, and proteins fragmented in parallel. Sponsors: Dr. John Garavelli is assisting us by incorporating the RESID database of post-translational modifications. We gratefully acknowledge these sources of generous support: * Searle Scholars Program and The Chicago Community Trust * The Burroughs Wellcome Fund * The University of Illinois

Proper citation: NeuroProSight (RRID:SCR_008632) Copy   

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http://www.zincfingertools.org

This site provides several tools for selecting zinc finger protein (ZFP) target sites and for designing the proteins that will target them. These ZFPs can be fused with effector domains that confer transcriptional activation or repression activity as well as catalytic functions.

Proper citation: Zinc Finger Tools (RRID:SCR_008598) Copy   

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http://nengo.ca

A software package for modelling large networks of neurons (typically hundreds or thousands), using spiking point-neuron models. Nengo is designed around the neural engineering framework (NEF). This is a mathematical framework that describes how neurons interact to represent information, perform computations, and behave dynamically. This framework has been used to develop sophisticated models of spatial working memory, probabilistic sound localization, and lamprey locomotion, among others. Nengo makes it easy for beginners to develop models using the NEF. If you accept defaults for spiking models, tuning curves, firing rates, etc. then you can have a rough approximation of a complex system assembled and running in minutes. Nengo also makes it easy for experts to do advanced work with the NEF. The design carefully encapsulates separable aspects of model behaviour, so that it is highly customizable and easy to extend.

Proper citation: Nengo (RRID:SCR_008631) Copy   

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http://alford.bios.uic.edu/index.html

We are principally interested in mechanisms of short-term synaptic plasticity and the impact of that plasticity on function in the nervous system. For our research we use two model vertebrate systems. A simple vertebrate model that affords us some fundamental advantages in this research is the lamprey central nervous system. The lamprey has a central nervous system that is very simple for a vertebrate and which may be kept alive, isolated but otherwise intact, for a number of days. Additionally, a group of axons in the spinal cord are very large and contain presynaptic structures that are exceptionally accessible to the experimentalist. This combination of features enables us to investigate synaptic plasticity at great detail and to determine its role in motor control. We have focused on the means by which G protein coupled receptors mediate enhancement and inhibition of glutamate release. We have identified a direct target for Gbg on the SNARE complex, the machinery for fusion of synaptic vesicles More recently we have utilized the rat hippocampus to determine whether similar mechanisms of synaptic plasticity are present in the mammalian brain. We have begun to focus on the role of kinase activation and short-term modification of transmitter release, in addition to how these modifications can alter the formation of memory during induction phases of long-term plasticity. Available software includes that for Electrophysiological Analysis, Image Analysis, and Confocal Software.

Proper citation: Alford Laboratory (RRID:SCR_008634) Copy   

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http://www.numpy.org

NumPy is the fundamental package needed for scientific computing with Python. It contains among other things: * a powerful N-dimensional array object * sophisticated (broadcasting) functions * tools for integrating C/C and Fortran code * useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Sponsored by ENTHOUGHT

Proper citation: NumPy (RRID:SCR_008633) Copy   

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http://www.wma.net

An organization that promotes the highest possible standards of medical ethics. The WMA provides ethical guidance to physicians through its Declarations, Resolutions and Statements. These also help to guide National Medical Associations, governments and international organizations throughout the world. The Declarations, Resolutions and Statements cover a wide range of subjects, including an International Code of Medical Ethics, the rights of patients, research on human subjects, care of the sick and wounded in times of armed conflict, torture of prisoners, the use and abuse of drugs, family planning and pollution.

Proper citation: World Medical Association (RRID:SCR_008592) Copy   

•   Source: SciCrunch Registry