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The Computation and Neural Systems degree program is organized jointly by the Division of Biology, the Division of Engineering and Applied Science, and the Division of Physics, Mathematics and Astronomy. It is the program''s objective to provide a broad knowledge of this inherently multidisciplinary field, while at the same time requiring an appropriate depth of knowledge in the particular field of the thesis research. For example, a student working on cooperative circuits for early visual processing will also develop an in-depth knowledge of the anatomy and electrophysiology of early visual areas and a knowledge of visual psychophysics. A student working on olfactory cortex electrophysiology and its simulation would include the study of concurrent processing and the ethology of olfaction, and the relevant knowledge of dynamical and collective systems. A student working on the theory of complex systems could study collective and statistical properties of physics as well as the anatomical and algorithmic structure of biological and applied networks. Sponsors: The computational and neural systems is funded by the California Institute of Technology.
Proper citation: Computational and Neural Systems (RRID:SCR_008316) Copy
A commercial software provider designed for legal, risk management, corporate, government, law enforcement, accounting, and academic markets. Sponsors: This resource is Reed Elsevier, Inc. Keywords: Workflow, Professional, Legal, Risk, Management, Corporate, Government, Law, Enforcement, Accounting, Academic, Technology, Information,
Proper citation: LexisNexis (RRID:SCR_008433) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 31, 2022. The UCSD CFAR/VMRF Molecular Biology Core (MBC) is a service core designed to facilitate and support HIV/AIDS research at the University of California San Diego (UCSD), the VA San Diego Healthcare System (VASDHCS), the Veterans Medical Research Foundation (VMRF), the UCSD Antiviral Research Center (AVRC), the Scripps Research Institute, and others in the San Diego HIV/AIDS research community. The MBC provides a variety of services, including DNA sequencing, viral DNA and RNA quantification, cDNA microarray analysis of herpesvirus expression, lentiviral vectors, RNAi design and synthesis, custom vector and plasmid design and construction, plasmids and other reagents of interest to HIV/AIDS research, shared access to computational biology software, and a variety of other services. The core is operated in association with the VMRF, the UCSD AIDS Research Institute (ARI), the VASDHCS, and the VA Research Center for AIDS and HIV Infection (RACHI). The VMRF/CFAR MBC is open to all UCSD, VA, and VMRF investigators as well as those from outside institutions. Keywords: Biology, Research, Medical, Molecular, DNA, Sequencing, Healthcare, RNA, DNA, cDNA, Microarray, Analysis, Herpesvirus, Expression, Lentiviral,
Proper citation: UCSD Center for AIDS Research Molecular Biology Core (RRID:SCR_008435) Copy
TRACK-HD is a multi-centermulti-national prospective, observational biomarker study of premanifest and early stage HD with no experimental treatment. Objectives: - determine what combination of measures is the most sensitive for detecting change over the natural course of premanifest and early HD - to validate these as potential outcome measures for use in future therapeutic trials Design: - focused on intensive battery of novel assessments - extensive annual assessments - dynamic and fluid protocol - robust evidence-based measures TRACK-HD is a major new international study of Huntingtons disease. It aims to be the most comprehensive study of premanifest and early HD, and will define the best combination of assessments to be used in clinical trials of disease-modifying treatments in HD. TRACK-HD began in January 2008 and involves 360 subjects at 4 sites internationally. Sponsors: This resource is supported by The UK Medical Research Council (MRC), CHDI Foundation, Inc., The Euro-HD Network, The Wellcome Trust, The Department of Health, The Huntingtons Disease Association, and The Brain Research Trust. Keywords: Biomarker, Experimental, Treatment, Research, Therapeutic, Trail, Hunginton''s, Disease, Health,
Proper citation: Track-HD (RRID:SCR_008397) Copy
http://ipmb.sinica.edu.tw/affy/
Affymetrix Gene Expression Service Lab, AGESL was established by IPMB, IMB and IBS, Academia Sinica and opened for service in June 2004. The lab provides a full service from quality control of customer-provided RNA samples to raw data acquisition, including Affymetrix recommended QC procedures, cDNA synthesis, in vitro transcription, fragmentation, hybridization, washing, staining and scanning. Sponsors: This resource is supported by Affymetrix, Inc. Keywords: Gene, Expression, Service, Laboratory, RNA, Data, Synthesis, cDNA, In vitro, Transcription, Fragmentation, Hybrdization, Washing, Staining, Scanning,
Proper citation: Affymetrix Gene Expression Service Lab (RRID:SCR_008396) Copy
http://www.youtube.com/education?b=400
This resource is geared towards providing educational video in various fields. All the videos are compiled from various sources and are freely accessible. Some of the topics covered are: - Business - Education - Engineering - Fine Arts & Design - Health & Medicine - History - Humanities - Journalism & Media - Law - Literature - Mathematics - Science - Social Science Sponsors: This resource is supported by YouTube, LLC.
Proper citation: YouTube Educational Portal (RRID:SCR_008310) Copy
http://www.loni.usc.edu/Software/jViewbox
A portable software framework for medical imaging research. jViewbox consists of a set of Java classes organized under a simple but extensive API that provides the core functionality of 2D image presentation needed by most imaging applications. It follows Java's Swing model closely to make it easy for application developers to build GUIs where end users can use various tools in a tool bar to manipulate the image displays. No optional add-ons or native code is used, which makes jViewBox compatible with any standard Java 2 Runtime Environment (version 1.3 or later).
Proper citation: jViewbox (RRID:SCR_008274) Copy
http://salilab.org/modeller/modeller.html
Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms.
Proper citation: MODELLER (RRID:SCR_008395) Copy
http://www.fa-petition.org/en/attivita/progetti2008.html
The aim of this resource is to facilitate and promote, even through fund-raising, the scientific research for the treatment of Friederich''s Ataxia. The mission of this portal is to: - To distribute information to the people affected by the disease and to make the general population aware. - Promote, fund and support the diagnosis, research, cure and potential treatments. - Promote the cooperation with other voluntary associations both national and international. Sponsors: This resource is supported by the RUDI Committee. Keywords: Research, Diagnosis, Cure, Treatment, Disease, Scientific, Friederich''s Ataxia,
Proper citation: ATASSIA DI FRIEDREICH - PROGETTI 2006 (RRID:SCR_008391) Copy
Center for the study of non-human primates. Its mission is the study and use of non-human primates as models for studies of social and biological interactions and for the discovery of methods of prevention, diagnosis and treatment of diseases that afflict humans. Through the stewardship of three unique facilities—Cayo Santiago Field Station, Sabana Seca Field Station, and the Laboratory of Primate Morphology supports a diverse range of research programs that enhance understanding of primate biology and behavior, with direct applications in biomedical and translational research.
Proper citation: Caribbean Primate Research Center (RRID:SCR_008345) Copy
The Lausanne Genomics Technologies Facility (GTF) is a genomic technologies core laboratory serving the Lausanne and Lemanic region research community. It is housed in and administered by the Center for Integrative Genomics. The GTF offers a range of microarrays services, including : providing access to the instrumentation and the consumables that are required for the use of the pre-printed oligonucleotide microarrays available from Affymetrix and Illumina as well as miRNA gene microarrays from Agilent Technologies providing access to and supporting applications using the Illumina Genome Analyzer 2 ultra high throughput DNA sequencing platform providing access to the instrumentation and the consumables that are required for performing quantitative real-time PCR analyses using the Applied Biosystems 7900HT Sequence Detection System. providing bioinformatics support and consultation services at the stages of experimental design, data collection and storage, image analysis and data analysis acting as a center of experience, expertise and training in microarray and quantitative PCR technologies and methodologies. Laboratory space and computer workstations are available to users wanting to perform the experiments and/or analyses in the facility. The GTF also acts as an information clearing house for the user community by providing a forum for the sharing of methods, protocols and experience generated by the GTF and community scientists using microarray and quantitative PCR technology investigating and implementing, when appropriate, microarray-based methods for applications other than gene expression monitoring (e.g. SNP detection) participating in the evaluation of new RNA expression profiling and nucleic hybridization detection technologies as they develop and incorporate the appropriate technologies into the services offered by the facility
Proper citation: Lausanne Genomic Technologies Facility (RRID:SCR_008468) Copy
http://edge.oncology.wisc.edu/edge.php
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. EDGE is a scientific resource for toxicology-related gene expression information. The site contains databases and analyses of gene expression studies following exposure to a variety of chemicals or physiological changes. The ultimate goal of the EDGE is to map transcriptional changes from chemical exposure that will someday be used as a diagnostic fingerprint to predict toxicity as well as provide valuable insights into the basic molecular changes responsible. EDGE gives you the ability to easily answer the following fundamental questions about your data 1. Can I compare transcriptional profiles across treatments? 2. What genes respond to my treatment? 3. What influences my favorite gene(s)? One of the major objectives of toxicology is to understand the adverse health effects that result from exposure to foreign chemicals. The traditional method for assessing the toxicity of a test chemical is very resource intensive; requiring the commitment of large amounts of money, time, and animals. According to the National Toxicology Program (NTP), each chemical study requires between 2 and 4 million dollars and several years to complete. Due to the cost and labor intensive nature of these studies, the number of chemicals currently tested by the NTP stands at less than 500. Given these statistics and the fact that there are approximately 70,000 chemicals in commerce today, it is increasingly apparent that alternative methods for assessing toxic potential must be explored if a significant portion of the remaining chemicals is to be tested. One potential solution is to develop a comprehensive database that describes alterations in gene expression resulting from chemical exposure. The pattern of transcriptional activity will not only be highly sensitive indicator of chemical exposure, but that this pattern will be diagnostic for mechanistically linked toxicants. In our laboratory, we have chosen to address this problem through a combination of high throughput sequencing of expressed sequence tags (ESTs) and construction of custom toxicology-related cDNA microarrays derived from the unique ESTs identified in the sequencing effort. By using this approach, we can simultaneously develop a quantitative gene expression profile using ESTs and the reagents for further analyzing these changes in a rapid, highly parallel manner. In addition, the expression profiles are not biased for preselected favorite genes. The resulting gene expression pattern can then be used as diagnostic fingerprint to predict toxicity and/or carcinogenicity as well as provide valuable insight into the basic biochemical and molecular changes responsible for toxicity. Submission of total RNA for Bradfield Lab Microarray Microarray comparisons are made between untreated, control animals and animals treated with ONE treatment. Please make sure the RNA submitted adheres to this experimental design. Necessary information is available on the site.
Proper citation: EDGE: Environment, Drugs and Gene Expression (RRID:SCR_008187) Copy
http://sig.biostr.washington.edu/projects/fm/FME/index.html
The Foundational Model Explorer (FME) is an internet based software application developed for viewing the content and organization of the Foundational Model of Anatomy Ontology (FMA). The initial purpose of the FME was to provide a simple and intuitive interface to the FMA for domain experts, in the field of anatomy, participating in the evaluation of the FMA. The FME also provides an easily available method of exploring the FMA to individuals or groups considering the adoption of the Foundational Model of Anatomy knowledge base. The FME display consists of two panes: a hierarchical tree may be opened up in the pane on the left side; if a class is selected in the hierarchical tree, the pane on the right side displays the information that has been entered in the FMA for that class. The information associated with a given class is organized in so-called slots. Each slot has a name (e.g., Definition, Parts) and some content, which is that particular slots value (e.g., the English definition and the names of parts of the selected class, respectively). For an explanation of the interactive features of the FME, see the Knowledge Navigation Section. For a guided tutorial check out the Conducted Tour. In the left pane, the default tree is a subclass hierarchy, based on the -is a- or -kind of- relationship; it is the instantiation of the Anatomy taxonomy (At) component in the high level scheme of the Foundational Model of Anatomy. Apart from the slots Preferred Name and Synonyms, other slots relate to the Anatomical Structural Abstraction (ASA) component in the FMAs high level scheme. Hierarchies based on various part-whole relationships can also be opened up in the left pane. Once a class has been highlighted in the subclass hierarchy, you can choose a relationship from a drop down list labeled Select navigation tree type. Some other transitive relationships (e.g., -branch of- and -tributary of-) are also available. The Search facility matches a search term to the preferred name, as well as to the Latin name, or synonym of an FMA class (if such exist). The tree is expanded to reveal the matching class and the information about this class is displayed. The wildcard * is allowed in the search term and will match to any sequence of characters. For example the search term h*d matches the class names Head and Hepatic cord (amongst others). The search function is not case sensitive. If more than one class name matches with the search term, a list of matching terms is presented for the user to choose between.
Proper citation: Foundational Model Explorer (RRID:SCR_008189) Copy
Griffin (G-protein-receptor interacting feature finding instrument) is a high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight. This system consists of two parts: 1) HMM section using family specific multiple alignment of GPCRs, 2) SVM section using physico-chemical feature vectors in GPCR sequence. G-protein coupled receptors (GPCR), which is composed of seven transmembrane helices, play a role as interface of signal transduction. The external stimulation for GPCR, induce the coupling with G-protein (Gi/o, Gq/11, Gs, G12/13) followed by different kinds of signal transduction to inner cell. About half of distributed drugs are intending to control this GPCR - G-protein binding system, and therefore this system is important research target for the development of effective drug. For this purpose, it is necessary to monitor, effectively and comprehensively, of the activation of G-protein by identifying ligand combined with GPCR. Since, at present, it is difficult to construct such biochemical experiment system, if the answers for experimental results can be prepared beforehand by using bioinformatics techniques, large progress is brought to G-protein related drug design. Previous works for predicting GPCR-G protein coupling selectivity are using sequence pattern search, statistical models, and HMM representations showed high sensitivity of predictions. However, there are still no works that can predict with both high sensitivity and specificity. In this work we extracted comprehensively the physico-chemical parameters of each part of ligand, GPCR and G-protein, and choose the parameters which have strong correlation with the coupling selectivity of G-protein. These parameters were put as a feature vector, used for GPCR classification based on SVM.
Proper citation: G protein receptor interaction feature finding instrument (RRID:SCR_008343) Copy
http://www.cff.org/treatments/Pipeline/
The Cystic Fibrosis Foundation has built a dynamic pipeline for the development of more new potential cystic fibrosis (CF) therapies than ever before. To treat a complex disease like CF, therapies must target problems in the airways and the digestive system. In the CF drug development pipeline, there also are promising new therapies designed to rectify the cause of CF a faulty gene and/or its faulty protein product. Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system of about 30,000 children and adults in the United States (70,000 worldwide). A defective gene and its protein product cause the body to produce unusually thick, sticky mucus that: clogs the lungs and leads to life-threatening lung infections; and obstructs the pancreas and stops natural enzymes from helping the body break down and absorb food. In the 1950s, few children with cystic fibrosis lived to attend elementary school. Today, advances in research and medical treatments have further enhanced and extended life for children and adults with CF. Many people with the disease can now expect to live into their 30s, 40s and beyond.
Proper citation: Drug Development Pipeline (RRID:SCR_008464) Copy
http://www.xiphophorus.txstate.edu/
Supplier of xiphophorus (platyfish or swordtails) from pedigreed parental lines, representing variety of species. In addition to supplying strains and providing consultation on husbandry and genetic questions, the XGSC produces custom interspecies hybrids (both first generation F1, and backcross hybrid generation BC1) for a variety of projects.
Proper citation: Xiphophorus Genetic Stock Center (RRID:SCR_008340) Copy
http://www.hopkins-abxguide.org/
Concise, clinically useful information for diagnosing, managing and treating infectious diseases in adults; however it does cover some pediatric topics including vaccines. It is designed for primary care providers and other non-infectious disease specialists as a tool that can be used at the point of care to assist in prescribing antibiotics.
Proper citation: ABX Guide (RRID:SCR_008214) Copy
http://www.nature.com/nature/supplements/collections/
This website provides summary collections written for a broad audience highlighting some of the significant advances in a particular field. These are not scientific articles although they may reference scientific work. Sponsors: This resource is supported by Nature.com
Proper citation: Nature Supplements: Collections archive (RRID:SCR_008337) Copy
NSDL is a digital library of exemplary resource collections and services, organized in support of science education at all levels. Starting with a partnership of NSDL-funded projects, NSDL is emerging as a center of innovation in digital libraries as applied to education, and a community center for groups focused on digital-library-enabled science education. The National Science Digital Library (NSDL) was created by the National Science Foundation to provide organized access to high quality resources and tools that support innovations in teaching and learning at all levels of science, technology, engineering, and mathematics (STEM) education. As a national network of learning environments, resources, and partnerships, NSDL seeks to serve a vital role as STEM educational cyberlearning for the nation, meeting the informational and technological needs of educators and learners at all levels. Educators need efficient and reliable methods to discover and use science and math materials that help them meet the demands of instruction, assessment, and professional development in an increasingly complex technology-based world. NSDL provides an organized point of access to: -High-quality STEM content aggregated from a variety of other digital libraries, NSF-funded projects, and NSDL-reviewed web sites. -Services and tools that enhance the use of this content in a variety of contexts. NSDL is designed primarily for K-16 educators, but anyone can access NSDL.org and search the library at no cost. Access to most resources discovered through NSDL is free; however, some content providers may require a login, or a nominal fee or subscription to retrieve their specific resources. NSDL serves as a nexus for educators, researchers, policy makers and the public by building bridges: -Between private sector and public interests by providing access to resources such as publisher'' journal articles, teacher-created lesson plans and real-time data sets from scientists -Between the scientific, research and educational communities by applying advanced technologies to stimulate new ways for educators and learners to access and use scientific information -Between teachers and learners at all levels, in all locations by supplying content and tools in open-access, non-proprietary formats in an easily accessible online environment. Sponsors: This work supported by the National Science Foundation under Grant No. 0733600, Grant No. 0424671, Grant No. 0227648, Grant No. 0227656, and Grant No. 0227888.
Proper citation: NSDL: The National Science Digital Library (RRID:SCR_008215) Copy
Center that supports studies of nonhuman primate models of human diseases, including common chronic diseases and infectious diseases and the effects that genetics and the environment have on physiological processes and disease susceptibility. SNPRC encourages the use of its resources by investigators from the national and international biomedical research communities.
Proper citation: Southwest National Primate Research Center (RRID:SCR_008292) Copy
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