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http://cran.r-project.org/web/packages/RJaCGH/index.html

Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.

Proper citation: RJaCGH (RRID:SCR_008381) Copy   

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http://www.cerc.utexas.edu/OnlineCall/

A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.

Proper citation: OnlineCall (RRID:SCR_008263) Copy   

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http://diademchallenge.org/data_sets.html

A software development competition, the DIADEM Challenge,to benefit the scientific community by encouraging the development of better software for automating three-dimensional reconstructions of neuronal arbors. The intent of the Sponsors is to ensure that the best software submitted for the competition is made available to the scientific community within a reasonable time and on reasonable terms. No purchase is necessary to enter or win. The competition will have two rounds. As of April 10, 2009, individuals and teams may register to participate in the competition and may download sets of image stacks (Data Sets) of non-human animal brains along with three-dimensional reconstructions for some of these Data Sets for training purposes. Submissions of software, including executable programs, supporting documentation, and reconstruction files for the Data Sets, must be uploaded to the competition website no later than April 9, 2010. In order to be eligible to win the competition, the individuals and at least one member of any teams whose submissions are selected for the Final Round (Finalists) must participate in the Final Round and scientific conference. Personal participation in the Final Round and scientific conference is important for two main reasons: first, because the Finalists software will be tested at the Final Round against additional Data Sets so that the judges can select a winner or winners, and second, because the larger scientific conference, of which the Final Round will be a part, is intended to foster extensive scientific interaction among neuroscientists and computational scientists, including plenary and poster sessions to discuss challenges, solutions, and future directions. There are 5 datasets, all of which have to be reconstructed for the qualifier phase. Once you have registered your group, dataset download information will be sent to you via E-mail. The 5 datasets are: - Cerebellar Climbing Fibers - Hippocampal CA3 Interneuron - Neocortical Layer 6 Axons - Neuromuscular Projection Fibers - Olfactory Projection Fibers Sponsors: The sponsors of this competition are: Allen Institute for Brain Science, Seattle, Washington; Howard Hughes Medical Institute (HHMI), Chevy Chase, Maryland; and Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia.

Proper citation: DIADEM Challenge: DIgital reconstruction of Axonal and DEndritic Morphology (DIADEM) Software Development Competition (RRID:SCR_008262) Copy   

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http://www.bioinformatics.kmutt.ac.th/list-of-courses-2/

This program is an international Bioinformatics course at KMUTT designed for students who desire focused training in the elements of computer science, biology and biochemistry needed for a successful career in this exciting new discipline. Students in this program will receive comprehensive training in genomics, algorithms for sequence analysis, database design and management, software engineering and programming (including web-based development). Each student will apply their skills to a practical project, where they will design and implement a solution to a real-world problem under the guidance of an experienced mentor in industry or academia. In order to receive a Masters degree, students must demonstrate mastery of the core subject matter (expected to maintain a minimum grade of B in all core courses) and reach a minimum TOEFL test score of 500 (paper) or 173 (computer) or equivalent prior to or on completion of the course. In 24 monhs students gain the knowledge and skills necessary to enter a career with industry or a career in research as a bioinformatics or biocomputing specialist. The program offers fifteen scholarships each year include tuition and fees plus an additional to cover living expenses for 24 months. :Keywords: Bioinformatics, Computer Science, Biology, Biochemistry, Genomics, Algorithms, Sequence, Analysis, Database, Design, Management, Software, Engineering, Programing, Industry, Academia, Master''s, :

Proper citation: Bioinformatic: Programs and Courses (RRID:SCR_008379) Copy   

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http://bioinfo.cipf.es/isacghtrac

Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.

Proper citation: IsaCGH (RRID:SCR_008375) Copy   

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http://flj.hinv.jp/

A human full-length cDNA sequence analysis database focused on mRNA varieties caused by variations of transcription start site (TSS) and splicing. Also available is ATGpr, a program for identifying the translational initiation codons in cDNA sequences. Data are derived from several full-length cDNA studies in Japan. Human gene number was estimated to be 20-25 thousand. However, the number of human mRNA varieties was predicted to be about 100 thousand. The varieties are thought to be caused by variations of TSS and splicing. In their previous human cDNA project, about 30 thousand of FLJ human full-length sequenced cDNAs were deposited to DDBJ/GenBank/EMBL, and they obtained about 1.4 million of 5''-end sequences (5''-EST) of FLJ full-length cDNAs from about 100 kinds of cDNA libraries consist of human tissues and cells constructed by oligo-capping method. The majority of the insert cDNA sizes were over 2 kb and the full-length rate of 5''-end was 90. And our FLJ cDNAs were covered about 80 of human genes. About 22 thousand of finished grades of full-length sequenced cDNAs were obtained in this project. The sequence analysis databases is focused on mRNA variations using human genome and cDNA sequences, FLJ full-length sequenced cDNAs, 5-ESTs of FLJ full-length cDNAs and other cDNA sequences described below. After those sequences were mapped onto the human genome sequences, clustering of the cDNA sequences were done based on the mapping results.

Proper citation: FLJ Human cDNA Database (RRID:SCR_008253) Copy   

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http://herpnet.org/

HerpNET is a collaborative effort by natural history museums to establish a global network of herpetological collections data. Sixty-four institutions are participating in the HerpNET community, with an open ended invitation to institutions who would like to join. Currently 56 institutions are available on the specimen searching portal, with data from over 5.5 million specimens available for searching. VertNet: The Future HerpNET, ORNIS, MaNIS and FishNet2 are taxon-based web portals that now serve georeferenced data on vertebrates from over 90 global institutions. Together these comprise VertNET, a cooperative project working to maintain and expand these distributed database projects. Future plans include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. Sponsors: This resource is supported by the National Science Foundation (NSF No. 0132303) and by a GBIF DIGIT .

Proper citation: HerpNET (RRID:SCR_008374) Copy   

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http://www.bioinf.uni-freiburg.de/Software

This resource takes you to the Server and Web-Applications of the University of Freiburg Bioinformatics Group. Sponsors: This resource is supported by University of Freiburg. Keywords: Server, Web application, Bioinformatics, Software,

Proper citation: University of Freiburg Bioinformatics Group: Servers and Web-Applications (RRID:SCR_008256) Copy   

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http://www.oege.org/software/hwe-mr-calc.shtml

This portal leads to the Chi-sq Hardy-Weinberg equilibrium test calculator for biallelic markers (SNPs, indels etc), including analysis for ascertainment bias for dominant/recessive models (due to biological or technical causes.) The purpose of this web program is for estimating possible missingness and an approach to evaluating missingness under different genetic models. Mendelian randomization (MR) permits causal inference between exposures and a disease. It can be compared with randomized controlled trials. Whereas in a randomized controlled trial the randomization occurs at entry into the trial, in MR the randomization occurs during gamete formation and conception. Several factors, including time since conception and sampling variation, are relevant to the interpretation of an MR test. Particularly important is consideration of the missingness of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. Testing for Hardy-Weinberg equilibrium (HWE) is a genetic approach that permits evaluation of missingness. Through this tool, the authors demonstrate evidence of nonconformity with HWE in real data. They also perform simulations to characterize the sensitivity of HWE tests to missingness. Unresolved missingness could lead to a false rejection of causality in an MR investigation of trait-disease association. These results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. Sponsors: This resource is supported by an Intermediate Fellowship (grant FS/05/065/19497) from the British Heart Foundation.

Proper citation: Hardy-Weinberg Equilibrium Calculator (RRID:SCR_008371) Copy   

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http://eldermet.ucc.ie

Latest publications: ELDERMET research has recently been published in the Proceedings of the National Academy of Sciences (USA). This work focuses on the composition and stability of the intestinal bacteria in older Irish adults. Read the paper here. Would you like to be part of ELDERMET? We are currently looking for people, aged 65 years or older, living in the community. All we ask is that you live in the Cork area, or are willing to travel to Cork, and have recently (within the last two/three weeks) taken any kind of antibiotic. It doesnt matter if you are still taking the antibiotic, as long as the finishing date isnt more than four weeks before your first visit to ELDERMET. ELDERMET Objectives To assess the composition of the faecal microbiota of elderly volunteers in the Irish population, using state-of-the-art molecular techniques. To correlate diversity, composition, and metabolic potential of the faecal microbial metagenome with health, diet and lifestyle indices that are a) likely to be influenced by the microbiota or b) to influence the microbiota. To develop recommendations for specific dietary ingredients, foodstuffs, functional foods and/or dietary supplements, that will improve the health of elderly consumers. To provide evidence-based recommendations for prospective studies to determine the molecular mechanisms for health improvements promoted by specific food ingredients that modulate components of the microbiota. ELDERMET Rationale The human intestinal microbiota is made up of approximately 1000 genetically unique organisms (phylotypes ) [1]. The bacteria present in the intestine make an important contribution to: metabolism executed in the gut [2] health, in diverse activites from pain perception [3] to cognitive function [4]. There is an increasing body of evidence linking alterations in the human gut microbiota with Inflammatory Bowel Disease [5, 6] and Irritable Bowel Syndrome [7]. The changing pattern of the gut microbiota in elderly subjects [8, 9] may be linked to host changes such as immunosenescence, increased susceptibility to disease and potentially systemic effects. The composition of the intestinal microbiota may be modulated by dietary components including prebiotics [10]. ELDERMET will determine the baseline composition of the gut microbiota of several hundred elderly Irish subjects using a combination of traditional culutre and molecular (culture-independent) methodologies. ELDERMET will explore potential correlations between microbiota composition and a range of health indices; cross-referencing data to dietary intake. Data will be analyzed in the context of the related FHRI projects in Nutrigenomics, Food Consumption, Food Safety, and Diet-Health. ELDERMET will provide recommendations to all stakeholders (including health practitioners and the health service, the food industry and the general public) on how to improve health based on defined modifications to dietary intake. Sponsor. This work is supported by the Goverment of Ireland Department of Agriculture Fisheries and Food/Health Research Board Food for Health Research Initiative award to the ELDERMET project as well as by a Science Foundation Ireland award to the Alimentary Pharmabiotic Centre. M.J.C. is now funded by a fellowship from the Health Research Board of Ireland.

Proper citation: ELDERMET Gut microbiota as an indicator and agent of nutritional health in elderly Irish subjects (RRID:SCR_008492) Copy   

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http://www.hopkins-hivguide.org/

Launched in 2004, the HIV Guide is a single disease resource, with two main parts: the HIV database, which is accessed by searching on diagnosis, drug name, pathogen, or management or by accessing the resistance tool, and there are also browsable areas of the site, which include news, features, continuing medical education programs and other types of additional readings and information. Guides are authored by academic clinicians and subject to rigorous peer review. You may browse the guide by: Diagnosis Covering opportunistic infections, malignancies, and complications of therapy. Drugs Includes indications, dosing, drug interactions, and author recommendations. Pathogen - Describes microbiology, clinical syndromes, and therapy. Management Including antiretroviral therapy guidelines and strategies. Resistance Tool Provides up-to-date interpretation of genotypic resistance test results. Whether searching for a drug, a pathogen, a diagnosis, or a management issue, your search results will be delivered in a concise and standard form designed to give you the most clinically useful information first, with the option to go deeper if you choose. If you search by diagnosis, you will receive a page listing points covering establishment of a diagnosis, related pathogens, treatment recommendations, issues to consider on follow up, references and more. At each step, we provide you immediately with the information you need to treat the diagnosis and give you the option to read more or more deeply if you choose. On the diagnosis page, you are also provided with links to the information sheet for each drug that may be prescribed, and if you indicate which drug you intend to use, you will be provided with relevant drug selected comments. If you search by drug, you will receive a page listing FDA indications, usual adult dosing, adverse drug reactions, drug interactions, spectrum, and forms. You are also able to access full pharmacological information (mechanism, absorption, Cmax, volume of distribution, protein binding, metabolism/excretion, t _, dosing for glomerular filtration of 50-80, dosing for glomerular filtration of 10-50, dosing for glomerular filtration of <10 ml/min, dosing in hemodialysis, dosing in peritoneal dialysis, dosing in cavh, dosing for decreased hepatic function, pregnancy risk, and breast feeding compatibility). If you search by pathogen, you will receive a page covering the microbiology, clinical relevance, sites of infection, drug selected comments, other information and references. You are also provided with links to information for each drug that may be prescribed, and if you indicate which drug you intend to use, you will be provided with the drug selected comments for that choice. If you search by management, you will receive a page listing definition, indications, and clinical recommendations and additional details, including references. If you click on more wherever it appears on a page, you will find more detailed material about the topic. In addition, the HIV Guide homepage contains a Features section and Literature Review that contain synopses and articles about pertinent topics. The Publications section also provides .pdf versions of the Hopkins HIV Report. Prices represent the cost per unit specified, reflecting the Average Wholesale Price (AWP). AWP prices are taken from the Red Book, manufacturer information, and the McKesson database. These prices are updated every six months. We have listed up to 10 FDA-approved indications for uses of drugs. Though in some cases more may exist, for brevity and formatting issues authors and editors have chosen what they deem the most important. Also listed are disease states for which a drug may be likely prescribed regardless of FDA approval status (see Non-FDA approved uses). The HIV Guide is primarily focused on adult care but does cover issues of perinatal transmission. The material presented on this site represents the considered opinion of the Hopkins expert listed as the author of the module as of the date indicated. The reference section contains an annotated list of the articles that the author considers to be most relevant to the topic. Where authoritative guidelines exist, such as CDC, IDSA or Medical Letter guidelines, they are referenced and discussed along with the author''s recommendations presented.

Proper citation: HIV Guide (RRID:SCR_008252) Copy   

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http://www.jneurosci.org/supplemental/18/12/4570/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest.

Proper citation: Hippocampal Slice Wave Animations (RRID:SCR_008372) Copy   

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http://www.agingintervention.org/

A 501(c)(3) non-profit organization that gives out grants created to develop new therapies to control and reverse the causes of aging, as well as treat and prevent the diseases of aging. The goal is to eventually control the processes of aging, reverse their effects, and stay younger longer and ultimately create indefinite youthful, happy and productive lifespan using innovative scientific methods that are under development today in biotech companies and research labs around the world. The foundation also offers education on what we can do now to stay younger, live longer and be happier while new therapies are being developed.

Proper citation: Aging Intervention Foundation (RRID:SCR_008288) Copy   

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http://www.track-hd.net

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   

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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   

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http://www.accelrys.com/products/downloads/ds_visualizer/

A life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Discovery Studio makes it easier to examine the properties of large and small molecules, study systems, identify leads and optimize candidates. Discovery Studio ADME Descriptors allow scientists to eliminate compounds with unfavorable ADME characteristics early in the discovery process and evaluate proposed structural refinements prior to synthesis. Applications of predictive ADME include pharmaceutical, cosmeceutical, and environmental sciences.

Proper citation: Discovery Studio Visualizer (RRID:SCR_008398) Copy   

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http://abgent.com

Antibody supplier.

Proper citation: Abgent (RRID:SCR_008393) Copy   

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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   

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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   

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http://biolit.ucsd.edu/doc/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 16, 2016. The establishment of open access literature makes it possible for knowledge to be extracted from scholarly articles and included in other resources. BioLit aims to extract database identifiers and rich meta-data from open access articles in the life sciences and integrate that information with existing biological databases. We have begun prototyping this effort using a clone of the RCSB Protein Data Bank, a database of macromolecular structures. Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We believe that the research community is ripe for a revolution in scientific communication and that the current generation of scientists will be the one to push it forward. These scientists, generally graduate students and new post-docs and have grown up with cyberinfrastructure as a part of their daily lives, not just a specialized aspect of their profession. They have a natural ability to do science in an electronic environment without the need for printed publications or static documents and, in fact, can feel quite limited by the traditional format of a publication. Perhaps most importantly, they appreciate that the sheer amount of data and the number of publications is prohibitive to the traditional methods of keeping current with the literature. Fink, L., Bourne, P. Reinventing Scholarly Communication for the Electronic Age, CTWatch Quarterly, Volume 3, Number 3, August 2007., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BioLit (RRID:SCR_008270) Copy   

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