Curator Dashboard

Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A transgenic mouse supplier which develops mouse lines expressing genetically encoded calcium indicators (GECIs) and optogenetic effectors in lineages relevant to cardiac, vascular, lung and blood diseases. The mouse strains created are designed to allow for inter crossing resulting in co-expression of sensors with discrete emission wavelengths in interacting lineages (e.g. endothelial and smooth muscle cells), as well as optically compatible effector/detector pairs.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. The study contains six data sets: histology and immunohistochemistry, in situ hybridization, rna-seq, protein quantification by luminex, isoprostane quantification, and specimen metadata.

• Resource
• Aging
• 11 years ago - by Anonymous

Software library of sequence alignment algorithms implemented in Java.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Biospecimen and clinical data repository for researchers that includes tumor and normal tissue, blood samples, and other bio fluids. Samples are refrigerated, frozen, deep frozen, or frozen in liquid nitrogen. Four service lines are provided: ExpressBank offers access to biospecimens, which are collected under IRB-approved core protocol for future unknown research projects; Service Bank offers services such as biospecimen procurement, processing, and temporary banking; PathBank offers access to high-quality, annotated formalin-fixed paraffin-embedded (FFPE) tissues and H&E slides from Pathology department on fee-for-sample basis; and On-DemandBank allows targeted development of a temporary Biobank that strictly meets the specifications of an IRB-approved collection protocol of a sponsor on fee-for-service basis.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. A set of web-based resources provided by the Bioinformatics Resource Centers (BRCs), focusing on organisms considered as potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. It provides data sets of host responses to pathogens and genome data, as well as tools to analyze host responses to pathogens.

• Resource
• SciCrunch
• 11 years ago - submitted by Ko-Wei Lin

Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

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.

• Resource
• dkNET
• 14 years ago - by Anonymous

Flexible Structural Neighborhood is a database of structural neighbors of proteins as seen by FATCAT - a flexible protein structure alignment program. The server accepts either a protein (PDB ID) or a domain (SCOP ID) as a query. For the former case, the server first displays the information of chains and domains of a given protein. Afterwards, users can retrieve similar structures for a domain (if domain information is available, i.e., the protein is collected by SCOP), or for a chain otherwise. The protein structure database we collected for similar structure search includes a representative set at 90% sequence identity of SCOP domains, and of up-to-date PDB entries that are not included in the latest release of SCOP.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

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.

• Resource
• dkNET
• 14 years ago - by Anonymous

Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

International clinical research consortium dedicated to the clinical evaluation of novel tolerogenic approaches for the treatment of autoimmune diseases, asthma and allergic diseases, and the prevention of graft rejection. They aim to advance the clinical application of immune tolerance by performing high quality clinical trials of emerging therapeutics integrated with mechanism-based research. In particular, they aim to: * Establish new tolerance therapeutics * Develop a better understanding of the mechanisms of immune function and disease pathogenesis * Identify new biomarkers of tolerance and disease Their goals are to identify and develop treatment game changers for tolerance modulating therapies for the treatment of immune mediated diseases and disabling conditions, and to conduct high quality, innovative clinical trials and mechanistic studies not likely to be funded by other sources or to be conducted by private industry that advance our understanding of immunological disorders. In the Immune Tolerance Network's (ITN) unique hybrid academic/industry model, the areas of academia, government and industry are integral to planning and conducting clinical studies. They develop and fund clinical trials and mechanistic studies in partnership. Their development model is a unique, interactive process. It capitalizes on their wide-ranging, multidisciplinary expertise provided by an advisory board of highly respected faculty from institutions worldwide. This model gives investigators special insight into developing high quality research studies. The ITN is comprised of leading scientific and medical faculty from more than 50 institutions in nine countries worldwide and employs over 80 full-time staff at the University of California San Francisco (UCSF), Bethesda, Maryland and Benaroya Research Institute in Seattle, Washington.

• Resource
• dkNET
• 14 years ago - by Anonymous

Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 02, 2011. Notice: This domain name expired on 10/29/11 and is pending renewal or deletion PD-DOC is a portal and a database resource, hosting a database and linking to other databases and data sets of clinical and translational data. PD-DOC functions to organize and facilitate clinical and translational research in Parkinson's disease. The PD-DOC Database contains standardized data collected by user institutions on large numbers of patients with Parkinsons disease and other parkinsonian disorders. In some cases, data is obtained at a single point in time, while in others data is collected repeatedly over time. The PD-DOC Database is composed of the Core Data Set (CDS) which consists of those variables required to be gathered for each subject whose data is entered into the PD-DOC database. In 2005, working groups of Udall Center and invited experts deliberated to establish the components of each CDS section (e.g. General Clinical, Cognitive/Behavioral, Postmortem Brain Neuropathological Findings). The PD-DOC CDS was established and designed to optimize data analyses and data mining for large numbers of subjects participating in a variety of research studies. In most cases corresponding DNA samples are available form the NINDS Human Genetic Repository (at Coriell). Much of the website is publicly available for viewing. To request access to sections of the website dealing with downloading or requesting data, requesting a consultation, or submitting data or other information you will need to register. Before registering, you should read the PD-DOC Policies. Note that PD-DOC data can be used for research purposes only. Once your registration is successfully completed you will be automatically logged into the website.

• Resource
• SciCrunch
• 16 years ago - by Anonymous