Tools   Select Another Resource Report Type

http://estscan.sourceforge.net/

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics.

Proper citation: ESTScan (RRID:SCR_005742) Copy   

•   Source: SciCrunch Registry

http://www.alzheimers.org/clinicaltrials/

A database of Alzheimer's disease and dementia clinical trials currently in progress at centers throughout the U.S.

Proper citation: AD Clinical Trials Database (RRID:SCR_005863) Copy   

•   Source: SciCrunch Registry

http://www.louisiana.edu/

Public research university in Lafayette, Louisiana. It has the largest enrollment within the nine-campus University of Louisiana System and the second largest enrollment in Louisiana.

Proper citation: University of Louisiana; Louisiana; USA (RRID:SCR_005743) Copy   

•   Source: SciCrunch Registry

http://www.mellon.org/

The Andrew W. Mellon Foundation currently makes grants in five core program areas: * Higher Education and Scholarship * Scholarly Communications and Information Technology * Art History, Conservation, and Museums * Performing Arts * Conservation and the Environment Within each of its core programs, the Foundation concentrates most of its grantmaking in a few areas. Institutions and programs receiving support are often leaders in fields of Foundation activity, but they may also be promising newcomers, or in a position to demonstrate new ways of overcoming obstacles to achieve program goals. Our grantmaking philosophy is to build, strengthen and sustain institutions and their core capacities, rather than be a source for narrowly defined projects. As such, we develop thoughtful, long-term collaborations with grant recipients and invest sufficient funds for an extended period to accomplish the purpose at hand and achieve meaningful results.

Proper citation: Andrew W. Mellon Foundation (RRID:SCR_005864) Copy   

•   Source: SciCrunch Registry

http://simile.mit.edu/

SIMILE, a joint project conducted by the MIT Libraries and MIT CSAIL, was focused on developing robust, open source tools that empower users to access, manage, visualize and reuse digital assets. SIMILE seeks to enhance interoperability among digital assets, schemata/vocabularies/ontologies, metadata, and services. A key challenge is that the collections which must inter-operate are often distributed across individual, community, and institutional stores. We seek to be able to provide end-user services by drawing upon the assets, schemata/vocabularies/ontologies, and metadata held in such stores. SIMILE will leverage and extend DSpace, enhancing its support for arbitrary schemata and metadata, primarily though the application of RDF and semantic web techniques. The project also aims to implement a digital asset dissemination architecture based upon web standards. The dissemination architecture will provide a mechanism to add useful views to a particular digital artifact (i.e. asset, schema, or metadata instance), and bind those views to consuming services. To guide the SIMILE effort we will focus on well-defined, real-world use cases in the libraries domain. Since parallel work is underway to deploy DSpace at a number of leading research libraries, we hope that such an approach will lead to a powerful deployment channel through which the utility and readiness of semantic web tools and techniques can be compellingly demonstrated in a visible and global community. The SIMILE Project and its members are fully committed to the open source principles of software distribution and open development and for this reason, it releases the created intellectual property (both software and reports) under a BSD-style license. The SIMILE Project Team Members gladly welcome community efforts.

Proper citation: SIMILE (RRID:SCR_005862) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench

Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible,

Proper citation: CLENCH (RRID:SCR_005735) Copy   

•   Source: SciCrunch Registry

http://www.sbur.org/

The Society for Basic Urologic Research (SBUR) is a society of scientists whose expertise includes the study of urologic cancers (prostate, bladder, kidney, testis, penis), the biology of prostate growth, kidney and bladder function, autoimmune urologic diseases, infectious diseases, neuro-urologic diseases, male reproductive biology, infertility and erectile dysfunction. Members include molecular biologists, immunologists, epidemiologists, oncologists, biochemists and clinical urologic scientists. SBUR members serve on a wide variety of advisory panels, study sections, editorial boards and in the pharmaceutical industry. The SBUR organizes two annual meetings to share new findings at a multidisciplinary level, to promote interaction among members and other interested scientists and to highlight new areas of research and funding opportunities. The Society was organized to address the following: * To provide a forum for the presentation and discussion of basic scientific topics related to urology * To develop educational forums concerning scientific advancements related to the field of urology * To promote collaborative investigations among member scientists with an emphasis on the interchange of expertise among clinical and basic scientists * To promote the communication and interests of urologic disease investigators with national funding agencies, industry representatives and academic institutions with regards to urology related research * To serve as a resource for research information and expertise to clinical urologists through the American Urological Association

Proper citation: SBUR - Society for Basic Urologic Research (RRID:SCR_005856) Copy   

•   Source: SciCrunch Registry

http://www.auanet.org/content/homepage/homepage.cfm

The American Urological Association (AUA), founded in 1902, is the premier professional association for the advancement of urologic patient care, and works to ensure that its more than 18,000 members are current on the latest research and practices in urology. The AUA also pursues its mission of fostering the highest standards of urologic care by providing a wide range of servicesincluding publications, research, the Annual Meeting, continuing medical education (CME) and the formulation of health policy.

Proper citation: American Urological Association (RRID:SCR_005859) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cell-Analysis/Antibodies-and-Secondary-Detection.html

Supports research in cellular analysis, genomics, proteomics, and drug discovery. It has merged with Thermo Fisher Scientific. One of several brands under Thermo Fisher Scientific corporation.

Proper citation: Invitrogen Antibodies (RRID:SCR_008410) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ompc.juricap.com

OMPC aims to enable reuse of the huge open and free code base of MATLAB on a free and faster growing Python platform. Running Python and MATLAB in a single interpreter avoids issues with running two separate applications. Python adds general purpose programming libraries to the convenient syntax of the language of technical computing. OMPC is not an interpreter, it lets Python to do the work. This means that if Python gets faster OMPC gets faster too. OMPC translates the m-files preserving the structure of the original programs as much as possible. Although OMPC comes with a library that emulates the features of numerical array of MATLAB there is nothing that will stop you from running the translated code the way you like it. This means that you could run the OMPC generated code on IronPython, Jython, PyPy or whatever else if you write your own numerical class. Sponsors: This resource is supported by RIKEN Brain Science Institute.

Proper citation: An Open-Source MATLAB-to-Python Compiler (RRID:SCR_008409) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/chudler/ehc.html

This web site focuses on neuroscience, the study of the nervous system. Links on this page are limited to those Dr. Chundler finds to be the most interesting and useful.

Proper citation: Eric H. Chundlers Links (RRID:SCR_008328) Copy   

•   Source: SciCrunch Registry

http://www.uni-mannheim.de/fakul/psycho/irtel/cvd.html

This page leads you to some screen shots from the Color Vision Demonstrations program CVD for IBM PCs and compatibles as described in this reference: Irtel, H. (1992). Color-vision demonstrations on an IBM PC/AT with VGA. Behavior Research Methods, Instruments, & Computers, 24, 88-89. Note that in order to display these images correctly you need a true color display with 8 bits resolution per color channel.

Proper citation: Color Vision Demonstrations (RRID:SCR_008327) Copy   

•   Source: SciCrunch Registry

http://www.brl.ntt.co.jp/cs/human/index.html

This site provides information about the NTT Human and Information Science Laboratory. Technologies that enable users to get along well with information and technologies that can handle information properly on computers and networks are the keys to secure and high-quality information distribution services in a network society. In realizing those technologies, a comprehensive understanding of how human beings, the creators and the recipients of information, process information and novel principles for handling information are indispensable. From this viewpoint, the NTT Human and Information Science Laboratory has been pursuing scientific research in two areas: Sensory and Emotion Research, and Sensory and Motor Research. Sponsors: This resource is supported by NTT Communication Science Laboratories.

Proper citation: Human and Information Science Laboratory (RRID:SCR_008329) Copy   

•   Source: SciCrunch Registry

http://www.uow.edu.au/

Public research university in New South Wales, Australia which offers degree programs across a wide spectrum of disciplines, as well as providing research facilities to scientists

Proper citation: University of Wollongong; New South Wales; Australia (RRID:SCR_008322) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.cns.caltech.edu/

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   

•   Source: SciCrunch Registry