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http://genome.unmc.edu/ngLOC/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.

Proper citation: ngLOC (RRID:SCR_003150) Copy   

•   Source: SciCrunch Registry

http://treebase.org/treebase-web/

Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.

Proper citation: TreeBASE (RRID:SCR_005688) Copy   

•   Source: SciCrunch Registry

http://www.morphbank.net/

An NSF supported image repository of over 374,000 high-resolution photographs of approximately 4,000 species for research and education, used largely but not exclusively in the area of biodiversity research. Images can be annotated by users and browsed by specimen, view, taxonomy, location, collection, or annotation.

Proper citation: MorphBank (RRID:SCR_003147) Copy   

•   Source: SciCrunch Registry

https://neuroscienceblueprint.nih.gov/Resources-Tools/Blueprint-Resources-Tools-Library

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups.

Proper citation: Biomedical Informatics Research Network (RRID:SCR_005163) Copy   

•   Source: SciCrunch Registry

http://www.elra.info/

ELRA is the driving force to make available the language resources for language engineering and to evaluate language engineering technologies. In order to achieve this goal, ELRA is active in identification, distribution, collection, validation, standardization, improvement, in promoting the production of language resources, in supporting the infrastructure to perform evaluation campaigns and in developing a scientific field of language resources and evaluation. ELRA''s missions are to promote language resources for the Human Language Technology (HLT) sector, and to evaluate language engineering technologies. To achieve these two major missions, we offer a range of services, listed below and described in the Services around Language Resources section: - Identification of language resources - Promotion of the production of language resources - Production of language resources - Validation of language resources - Evaluation of systems, products, tools, etc., related to language resources - Distribution of language resources - Standardization The promotion of the production of language resources also includes our support of the infrastructure for evaluation campaigns and our support in developing a scientific field of language resources and evaluation, e.g. via the LREC conference. ELRA also regularly conducts market studies and surveys in the field of HLT, and publishes a quarterly newsletter, distributed not only to its members but also to a large number of people in the HLT community.

Proper citation: European Language Resources Association (RRID:SCR_004909) Copy   

•   Source: SciCrunch Registry

https://peerlibrary.org/

Open source project providing a collaborative layer of knowledge over academic publications by allowing users to share real-time highlights and annotations. Participate in open discussion that drives ideas and academia forward. It provides a supportive space to learn about research and ask questions of peers and experts. Follow authors and other users to understand their perspectives, make connections, and discover new ideas.

Proper citation: PeerLibrary (RRID:SCR_003812) Copy   

•   Source: SciCrunch Registry

http://sig.biostr.washington.edu/projects/MindSeer/index.html

A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start).

Proper citation: MindSeer (RRID:SCR_003019) Copy   

•   Source: SciCrunch Registry

http://vmd.vbi.vt.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs.

Proper citation: VMD (RRID:SCR_004905) Copy   

•   Source: SciCrunch Registry

http://www.pristionchus.org

This data resource is a genetic, molecular, and genomic toolkit that establishes one particular species, Pristionchus pacificus, as a major satellite system for evolutionary developmental biology. Users may download Pristionchus Sequences and use the Pristionchus pacificus genome browser where they may find gene or gene prediction data. Users can also use the BLAST feature, which allows users to search the assembly for position information of bacs, reads and contigs using the mapping tool. The center of the site's research is the evolutionary analysis of vulva formation. The general aim of the Department is to develop the nematode vulva as a suitable case study into the evolutionary alterations of developmental processes. By studying and comparing two distantly related species of the same phylum, such as P. pacificus and C. elegans, macroevolutionary alterations of developmental processes and mechanisms can be identified. The final goal of the Department is to achieve a comprehensive description of macro- and microevolutionary changes of developmental mechanisms at the molecular level in a phylogenetic and ecological context.

Proper citation: Pristionchus.org (RRID:SCR_003414) Copy   

•   Source: SciCrunch Registry

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

Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images.

Proper citation: TumorSim (RRID:SCR_002604) Copy   

•   Source: SciCrunch Registry

http://htseq.readthedocs.io/en/release_0.9.1/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

Proper citation: HTSeq (RRID:SCR_005514) Copy   

•   Source: SciCrunch Registry

http://www.ucdenver.edu/academics/colleges/medicalschool/departments/neurology/Pages/Chair.aspx

The Department is part of the University of Colorado Anschutz Medical Center and is one of the largest Academic Medical Centers between Chicago and the West Coast. The School of Medicine is in the top 25 schools nationally in NIH funding and includes numerous nationally recognized affiliated hospitals. Our Department is composed of over 30 primary faculty members whose clinical and research interests and activities encompass virtually all aspects of neurology. Faculty are integrated into functional units including Behavioral Neurology, Cerebrovascular Diseases, Epilepsy and Sleep Disorders, Infectious Disease, Movement Disorders, Multiple Sclerosis, Neuromuscular Disorders, Neuro-oncology, and Neuro-ophthalmology each of which strives to provide cutting-edge diagnostic and therapeutic services to patients and families dealing with neurological disease. Our faculty have clinical activities at four affiliated teaching hospitals (The Childrens Hospital, Denver Health Medical Center, Denver Veterans Affairs Medical Center, University Hospital), each of which brings unique clinical, educational, and research strengths to our program. Clinical, research and educational programs are closely linked to the Division of Pediatric Neurology of the Department of Pediatrics. The educational mission of the Department includes primary responsibility for the training of medical students in required neurology clerkships, an ACGME accredited Neurology Residency Training Program (16 positions), Clinical Fellowships (Behavioral Neurology, Cerebrovascular Disease, CNS Infections, Epilepsy, Movement Disorders, Neuromuscular Disease, MS) and both clinical and laboratory based fellowships in neurology research. The clinical enterprise includes busy outpatient, inpatient and consultation services, as exemplified by over 12,000 outpatient visits and over 800 annual admissions at UH.

Proper citation: University of Colorado School of Medicine Department of Neurology (RRID:SCR_005351) Copy   

•   Source: SciCrunch Registry

http://www.gene-talk.de

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations.

Proper citation: GeneTalk (RRID:SCR_005231) Copy   

•   Source: SciCrunch Registry

http://seer.cancer.gov/resources/

Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.

Proper citation: SEER Datasets and Software (RRID:SCR_003293) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.nl/QualitySNPng/

Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy.

Proper citation: QualitySNPng (RRID:SCR_002479) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/pbsim/

Software that simulates PacBio reads by using either a model-based or sampling-based simulation.

Proper citation: PBSIM (RRID:SCR_002512) Copy   

•   Source: SciCrunch Registry

http://biologicstylus.sourceforge.net/

Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python

Proper citation: Biologic Stylus (RRID:SCR_002991) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/news/media/audio/index.shtml

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Audio and video available from the National Institute of Mental Health (NIMH).

Proper citation: NIMH Multimedia (RRID:SCR_005467) Copy   

•   Source: SciCrunch Registry

http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/default.htm

Project to improve the microarray and next-generation sequencing technologies and foster their proper applications in discovery, development and review of FDA regulated products by developing standards and quality measures. Microarrays and next-generation sequencing represent core technologies in pharmacogenomics and toxicogenomics; however, before these technologies can successfully and reliably be used in clinical practice and regulatory decision-making, standards and quality measures need to be developed. Everyone is invited to participate in the MAQC project.

Proper citation: MAQC (RRID:SCR_002351) Copy   

•   Source: SciCrunch Registry

http://wiki.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3

3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010.

Proper citation: SpineSegmentation module for 3DSlicer (RRID:SCR_002593) Copy   

•   Source: SciCrunch Registry