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http://www.px.nsls.bnl.gov/

Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage.

Proper citation: Macromolecular Crystallography Research Resource (RRID:SCR_001442) Copy   

•   Source: SciCrunch Registry

https://medicine.yale.edu/keck/nida/yped/

Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards.

Proper citation: YPED (RRID:SCR_001436) Copy   

•   Source: SciCrunch Registry

http://www.anxietyaustralia.com.au/

Anxiety Treatment Australia provides information about anxiety disorders, the treatment options, psychologists around Australia who treat anxiety disorders, group therapy & workshops, support groups, articles, resources and links to other sites. Sponsors: his website is brought to you by Catherine Madigan, a Melbourne Clinical Psychologist who specializes in the treatment of Anxiety Disorders (ABN 51 109 368 630).

Proper citation: Anxiety Treatment Australia: Anxiety Disorder Help, Information and Psychologist List (RRID:SCR_001434) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/philips_users/

Communnity project to help support the efforts of investigators using Philips Healthcare systems. This clearingsite helps users find forums, mailinglists, etc. that support this community. If you have suggestions for inclusion, let the project admin know!

Proper citation: Philips Users Community (RRID:SCR_001438) Copy   

•   Source: SciCrunch Registry

http://type1diabetes.jax.org/

International repository for importation, curation, genotypic and phenotypic validation, cryopreservation, and distribution of mouse stocks of value to the type 1 diabetes scientific community holding over 250 genetically modified or congenic mouse stocks that are being used to dissect genetic and biologic features of T1D. They provide extensive genotypic and phenotypic quality control and genetic stabilization for these strains, as well as incidence studies when available. An added value of T1DR stocks is their ability to propel advances in related areas of science, including research in non-T1D autoimmunity and infectious diseases. The staff provides information and technical assistance regarding selection and use of existing T1DR models, and will provide limited support for development of new models considered to be of high-value for the T1D community. The resource includes strains generated at the Jackson Laboratory as well as strains donated by external scientists. Investigators are highly encouraged to donate a strain to ensure its preservation and availability to other researchers.

Proper citation: Type 1 Diabetes Resource (RRID:SCR_001475) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html

R package with tools for analyzing and visualizing bisulfite sequencing data.

Proper citation: bsseq (RRID:SCR_001072) Copy   

•   Source: SciCrunch Registry

http://www.diabetestrialnet.org/

International network of researchers who are exploring ways to prevent, delay and reverse the progression of type 1 diabetes. It is conducting clinical trials with researchers from 18 Clinical Centers in the United States, Canada, Finland, United Kingdom, Italy, Germany, Australia and New Zealand. In addition, more than 150 medical centers and physician offices are participating in the TrialNet network. Studies are available for people newly diagnosed with type 1 diabetes, as well as for relatives of people with type 1 diabetes who are at greater risk of developing the disease. This NIH-sponsored clinical trials network conducts studies designed to evaluate new approaches to prevent or ameliorate type 1 diabetes specifically by interdicting the type 1 diabetes disease process. These include interventions designed to decrease beta-cell destruction and/or enhance beta-cell survival. Studies are conducted in non-diabetic persons at risk of type 1 diabetes in an effort to delay the development of type 1 diabetes as a clinical disease; or (if initiated prior to appearance of autoimmunity) in an effort to delay the appearance of autoimmunity; or in individuals with type 1 diabetes who are either newly diagnosed or have evidence of sustained beta cell function. Studies include long-term follow-up of subjects developing type 1 diabetes. The TrialNet network also supports natural history and genetics studies in populations screened for or enrolled in studies conducted by the TrialNet study group. In addition, TrialNet will evaluate methodologies that enhance the conduct of clinical trials interdicting the type 1 diabetes disease process.

Proper citation: Type 1 Diabetes TrialNet (RRID:SCR_001508) Copy   

•   Source: SciCrunch Registry

http://www.statepi.jhsph.edu/ckid/

Prospective, observational cohort study of children with mild to moderate chronic kidney disease (CKD) to: (1) determine risk factors for progression of pediatric chronic kidney disease (CKD); (2) examine the impact of CKD on neurocognitive development; (3) examine the impact of CKD on risk factors for cardiovascular disease, and; (4) examine the impact of CKD on growth. The CKiD study population will include a cohort of 540 children, age 1 16 years, expected to be enrolled over a 24-month period.

Proper citation: CKID A Prospective Cohort Study of Kidney Disease in Children (RRID:SCR_001500) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html

R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.

Proper citation: R453Plus1Toolbox (RRID:SCR_001105) Copy   

•   Source: SciCrunch Registry

http://www.citregistry.org/

Collect, analyze, and communicate on comprehensive and current data on all islet/beta cell transplants in human recipients performed in North America, as well as some European and Australian centers to expedite progress and promote safety in islet/beta cell transplantation. This site serves as a repository for general information concerning protocols, clinical transplantation sites, publications, and other information of interest to the general community. Annual Reports are available. Islet/beta cell transplantation is a complex procedure with many factors contributing to the outcome. Compiling and analyzing data from all transplant centers in the US, Canada, as well as some European and Australian centers will accelerate the identification of both critical risk factors and key determinants of success and thereby guide transplant centers in developing and refining islet/beta cell transplant protocols. The inclusion of the term collaborative in the name of the Registry emphasizes the importance of collaboration in fulfilling the CITR mission and goals. Close collaboration with the transplant centers will ensure that relevant questions are addressed, that data submitted are accurate and complete, and that the needs of the transplant community are served. Information on how to participate as a CITR Transplant Center and to receive a transplant center application is available through the website. Progress in islet transplantation depends entirely on complete, high-quality medical data, including the information patients consented to report to the Collaborative Islet Transplant Registry. To make it as easy as possible to provide updated information about patient's health, an on-line questionnaire is available or patients can mail it to their transplant center. This information is very important in the continuing search for a cure for Type 1 diabetes.

Proper citation: Collaborative Islet Transplant Registry (RRID:SCR_001466) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CGEN.html

Software R package for analysis of case-control studies in genetic epidemiology.

Proper citation: CGEN (RRID:SCR_001251) Copy   

•   Source: SciCrunch Registry

http://www.morpholinodatabase.org/

Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password.

Proper citation: Morpholino Database (RRID:SCR_001378) Copy   

•   Source: SciCrunch Registry

http://www.g-node.org/projects/odml

Mark up language for collecting and exchanging metadata in an automated, computer-based fashion, developed for neuroscience, specifically, neurophysiology experiments. In odML arbitrary metadata information is stored as extended key-value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability.

Proper citation: Open metadata mark up language (RRID:SCR_001376) Copy   

•   Source: SciCrunch Registry

http://www.softgenetics.com/mutationSurveyor.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.

Proper citation: Mutation Surveyor (RRID:SCR_001247) Copy   

•   Source: SciCrunch Registry

http://genecodes.com/sequencher

Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data.

Proper citation: Sequencher (RRID:SCR_001528) Copy   

•   Source: SciCrunch Registry

http://www.findmice.org/index.jsp

Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known.

Proper citation: International Mouse Strain Resource (RRID:SCR_001526) Copy   

•   Source: SciCrunch Registry

http://www.genome.jp/kegg/expression/

Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.

Proper citation: Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) Copy   

•   Source: SciCrunch Registry

http://scitools.idtdna.com/analyzer/Applications/OligoAnalyzer/

Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration.

Proper citation: Integrated DNA Technologies OligoAnalyzer (RRID:SCR_001363) Copy   

•   Source: SciCrunch Registry

https://www.unafold.org/

Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows.

Proper citation: UNAFold (RRID:SCR_001360) Copy   

•   Source: SciCrunch Registry

http://isp.imm.dtu.dk/thor/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Center hosting a number of related projects concerning neural networks, functional neuroimaging, multimedia signal processing, and biomedical signal processing. Neuroinformatics is a research field rooted in classical disciplines like signal processing, biology, physics, computer science and engineering. Neuroinformatics combines learning from the brain and learning about the brain. By studying information processing in the brain neuroinformatics invents new computing paradigms (e.g., artificial neural networks) with the objective of understanding the dynamics of the conscious mind. Artificial neural networks is an active neuroinformatics research field, which combines many approaches to adaptive signal processing in solving real world problems. They began using neural networks for general nonlinear adaptive signal processing. Since 1991 the CONNECT groups have participated in the development of neural computing as an advanced, non-linear statistical tool, which has been applied to forecasting within dynamical systems, pattern recognition, and medical image analysis, particularly functional neuroimages. While neural computing has largely been viewed as a black box approach, they have initiated research aimed at opening this black box, using hypertext, multimedia, and interactivity. Their key objective is to convert abstract models into intuitive knowledge through interactive visualization.

Proper citation: THOR Center for Neuroinformatics (RRID:SCR_001400) Copy   

•   Source: SciCrunch Registry