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https://services.healthtech.dtu.dk/
Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.
Proper citation: DTU Center for Biological Sequence Analysis (RRID:SCR_003590) Copy
http://grants.nih.gov/podcasts/All_About_Grants/index.htm
The Office of Extramural Research (OER) presents conversations with NIH staff members. Designed for investigators, fellows, students, research administrators, and others, we provide insights on grant topics from those who live and breathe the information. In mp3 and updated monthly. Transcripts are also available. So You Wanna... Keep Up with What''''s Hot? Prepare a Successful Grant Application? Suggest a Topic? Understand How Your Grant is Reviewed? Be an NIH Investigator?
Proper citation: All About Grants Podcast (RRID:SCR_005621) Copy
A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.
Proper citation: 3D Slicer (RRID:SCR_005619) Copy
http://great.stanford.edu/public/html/splash.php
Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool
Proper citation: GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project to advance understanding of the neural mechanisms of vocal learning by providing a quantitative description of the relationship between physiological variables and vocal performance over the course of development in a songbird, the zebra finch. They propose to study vocal learning dynamically across neuronal and peripheral subsystems, using a novel collaborative approach that will harness the combined expertise of several investigators. Their proposed research model will 1) provide simultaneous measurements of acoustic, articulatory and electrophysiological data that will document the detailed dynamics of the vocal imitation process in a standardized learning paradigm; and 2) incorporate these measurements into a theoretical/computational framework that simultaneously provides a phenomenological description and attempts to elucidate the mechanistic basis of the learning process.
Proper citation: Zebra Finch Song Learning Consortium (RRID:SCR_006356) Copy
http://www.ebi.ac.uk/pdbe/emdb/
Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.
Proper citation: Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) Copy
http://grants.nih.gov/grants/oer.htm
OER serves as a vital interface between the NIH and the biomedical research community by guiding investigators through the process of attaining grants funding and helping them understand and navigate through federal policies and procedures. OER supports extramural research by providing policy and guidance to the 24 NIH Institutes and Centers that award grants. Extramural grants account for approximately 84 percent of NIH''s 29 billion budget. These are awarded to investigators throughout the U.S. and abroad. Approximately 10 percent of the NIH budget supports NIH intramural investigators, NIH staff who conduct research.
Proper citation: Office of Extramural Research NIH (RRID:SCR_006547) Copy
http://www.medschool.lsuhsc.edu/neuroscience/
Research center that takes multidisciplinary approach to neuroscience education and research. Research programs on molecular and cellular bases of neural diseases are the center of the innovative educational programs. Primary mission is to foster and conduct science that advances understanding of brain function and diseases that affect nervous system.
Proper citation: Louisiana State University School of Medicine Neurosciences Center (RRID:SCR_006446) Copy
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/
Consortium that puts sequences into a chromosome context and provides the best possible reference assembly for human, mouse, and zebrafish via FTP. Tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences.
Proper citation: Genome Reference Consortium (RRID:SCR_006553) Copy
http://www.nitrc.org/projects/gscca_2013/
Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.
Proper citation: Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) Copy
http://cerebrovascularportal.org
Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data.
Proper citation: Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) Copy
http://www.alliancegenome.org/
Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN).
Proper citation: Alliance of Genome Resources (RRID:SCR_015850) Copy
https://github.com/KravitzLab/fed/wiki
Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.
Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) Copy
http://www.genetherapyreview.com/gene-therapy-research
The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.
Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://emcore.ucsf.edu/cryoem-software
Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux.
Proper citation: MotionCor2 (RRID:SCR_016499) Copy
https://cm.jefferson.edu/rna22/
Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.
Proper citation: RNA22 (RRID:SCR_016507) Copy
https://tbportals.niaid.nih.gov
Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.
Proper citation: TB PORTALS (RRID:SCR_016594) Copy
https://www.ncbi.nlm.nih.gov/projects/mutagene/
Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.
Proper citation: MutaGene (RRID:SCR_016574) Copy
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