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https://gtexportal.org/home/

Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets.

Proper citation: GTEx eQTL Browser (RRID:SCR_001618) Copy   

•   Source: SciCrunch Registry

http://magest.hgc.jp/

A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future.

Proper citation: MAboya Gene Expression Patterns and Sequence Tags (RRID:SCR_000763) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/brands/thermo-scientific/molecular-biology.html#/legacy=fermentas.com

Web-based resource that provides an integrated set of tools for DNA sequence anlaysis, plasmid map creation, sequence viewing, and various biochemical calculations.

Proper citation: REviewer - sequence analysis tools (RRID:SCR_001336) Copy   

•   Source: SciCrunch Registry

http://www.cpctr.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Doumented on September 23,2022. The National Cancer Institute initially established the Cooperative Prostate Cancer Tissue Resource (CPCTR) to provide prostate cancer tissue samples with clinical annotation to researchers. The Resource provides access to formalin-fixed, paraffin-embedded primary prostate cancer tissue with associated clinical and follow-up data for research studies, particularly studies focused on translating basic research findings into clinical application. Fresh-frozen tissue is also available with limited clinical follow up information since these are more recent cases. The Resource database contains pathologic and clinical information linked to a large collection of prostate tissue specimens that is available for research. Researchers can determine whether the Resource has the tissues and patient data they need for their individual research studies. Consultation and interpretive services: Assistance is available from trained CPCTR pathologists. The CPCTR can provide consultative assistance in staining interpretation, and scoring, on a collaborative basis. Fresh Frozen and Paraffin Tissue: The resource has over 7,000 annotated cases (including 7,635 specimens and 38,399 annotated blocks). Tissue Microarrays (TMA): The CPCTR has slides from prostate cancer TMAs with associated clinical data. The information provided for each case on the arrays (derived from radical prostatectomy specimens) includes: age at diagnosis, race, PSA at diagnosis, tumor size, TNM stage, Gleason score and grade, and vital status and other variables.

Proper citation: CPCTR: Cooperative Prostate Cancer Tissue Resource (RRID:SCR_000803) Copy   

•   Source: SciCrunch Registry

http://compbio.dfci.harvard.edu/amp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.

Proper citation: Automated Microarray Pipeline (RRID:SCR_001219) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.

Proper citation: BLASTP (RRID:SCR_001010) Copy   

•   Source: SciCrunch Registry

http://blogs.plos.org/

PLoS Blogs has been set up to bring a select group of independent science and medicine bloggers together with the editors and staff who run our blogs. Our independent network is made up of writers who love science and medicine, and scientists and physicians that love to write. Here, you'll find an equal mix of blogs from journalists and researchers tackling diverse issues in science and medicine. There are three very distinct types of blogs on the PLoS Blogs network: the official PLoS blog, the PLoS journal blogs (collectively known as The PLoS Blogs), and blogs from the independent network (a.k.a. The PLoS Blogosphere) # The official PLoS blog: This content is produced, edited, and/or maintained by PLoS staff. # The journal blogs: This content is produced, edited, and/or maintained by PLoS journal staff: The current journal blogs are Speaking of Medicine (PLoS Medicine's blog) and everyONE (PLoS ONE's blog). # Our independent network of bloggers (The PLoS Blogosphere): This content is produced, edited, and/or maintained by the authors. * All of the content in The PLoS Blogosphere came from the minds of the authors. PLoS does not screen, edit, or otherwise meddle with content on the these blogs in any way. Our bloggers and our users are held to exactly the same standards, and the community guidelines apply to everyone that uses our site. If a blogger has posted content that you believe violates our site abuse policy, please contact PLoS. * Bloggers monitor their own comment threads: All comments will be reviewed by the author of the blog where you leave your thoughts. Just follow our simple community guidelines and we'll all get along just fine.

Proper citation: PLoS Blogs (RRID:SCR_001371) Copy   

•   Source: SciCrunch Registry

https://fungi.ensembl.org/Neurospora_crassa/Info/Index

It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available.

Proper citation: Neurospora crassa Database (RRID:SCR_001372) Copy   

•   Source: SciCrunch Registry

http://umcecaruca01.extern.umcn.nl:8080/ecaruca/ecaruca.jsp

A database of cytogenetic and clinical information on rare chromosomal disorders, including microdeletions and microduplications. The database is meant to be easily accessible for all participants, to improve patient care and collaboration between genetic centers, and collect the results of research and clinical features. The acronym ECARUCA stands for "European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations".

Proper citation: ECARUCA Project (RRID:SCR_000797) Copy   

•   Source: SciCrunch Registry

http://www.btool.org/WegoLoc

Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information.

Proper citation: WegoLoc (RRID:SCR_001402) Copy   

•   Source: SciCrunch Registry

http://mint.bio.uniroma2.it/

A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.

Proper citation: MINT (RRID:SCR_001523) Copy   

•   Source: SciCrunch Registry

http://www.drive5.com/muscle/prefab.htm

Downloadable data designed for testing multiple sequence alignment methods.

Proper citation: PREFAB (RRID:SCR_001009) Copy   

•   Source: SciCrunch Registry

http://www.ipha.ie/alist/ifpma-clinical-trials-portal.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. IFPMA Clinical Trials Portal is brought to you by IFPMA on behalf of its Member Companies and Associations. IFPMA Clinical Trials Portal ensures: a free and easy-to-use interface for patients and health professionals alike to ongoing clinical trials, clinical trial results and complementary information on related issues; non-promotional and reliable information; industry's commitment to the transparency of clinical trials. * Search by Medical Condition and Drug Name * Language Interfaces (En, Es, Fr, De, Jp) * Glossary and Easy Explanation of Medical Expressions * Geographical Search

Proper citation: IFPMA Clinical Trials Portal (RRID:SCR_000791) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-12/search?q=*

A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.

Proper citation: Integrated Models (RRID:SCR_001481) Copy   

•   Source: SciCrunch Registry

http://www.nsfgrfp.org/

The National Science Foundation's Graduate Research Fellowship Program (GRFP) helps ensure the vitality of the human resource base of science and engineering in the United States and reinforces its diversity. The program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master's and doctoral degrees in the U.S. and abroad. The NSF welcomes applications from all qualified students and strongly encourages under-represented populations, including women, under-represented racial and ethnic minorities, and persons with disabilities, to apply for this fellowship. Fellows share in the prestige and opportunities that become available when they are selected. Fellows benefit from a three-year annual stipend of $30,000 along with a $10,500 cost of education allowance for tuition and fees, a one-time $1,000 international travel allowance and the freedom to conduct their own research at any accredited U.S., or foreign institution of graduate education they choose. NSF Fellows are anticipated to become knowledge experts who can contribute significantly to research, teaching, and innovations in science and engineering. So that the nation can build fully upon the strength and creativity of a diverse society, the Foundation welcomes applications from all qualified individuals. Women, under-represented minorites and people with disabilities are encouraged to apply. Those with disabilities are additionally accommodated by the Foundation to provide for the most successful graduate experience possible. Sponsors: This program is supported by the National Science Foundation (NSF).

Proper citation: National Science Foundation Graduate Research Fellowship Program (RRID:SCR_001487) Copy   

•   Source: SciCrunch Registry

http://tobaccodocuments.org/datta

A database of information from the Center for Tobacco Use Prevention and Research. Materials include depositions, trial testimony and opening and closing statements, expert reports, jury instructs, and verdicts. Some transcripts are rough copies and others may be marked as confidential although they no longer retain that status. This resource is in French.

Proper citation: Ronald M. Davis Tobacco Deposition and Trial Testimony Archive (RRID:SCR_000795) Copy   

•   Source: SciCrunch Registry

http://igenbio.com/

A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement

Proper citation: ERGO (RRID:SCR_001243) Copy   

•   Source: SciCrunch Registry

https://parkinsontrial.ninds.nih.gov/about.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, futility study of minocycline and creatine in subjects with early untreated Parkinson's Disease (PD) or FS-I (Futility Study I). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. A Multicenter, Double-Blind, Futility Study of Minocycline and Creatine in subjects with early untreated Parkinson's Disease (PD) (FS-1).The primary objective of the study was to assess the impact of minocycline and creatine on the progression of PD in order to assess whether it was non-futile to proceed with further study of these agents. The progression of PD was measured by the change in total UPDRS score between the baseline visit and month 12 or the time of sufficient disability to require symptomatic therapy (last visit before subject goes on dopaminergic therapy), whichever occurs first. The additional follow-up of subjects until 18 months addressed the secondary objectives. The FS-1 study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).

Proper citation: NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study I (RRID:SCR_001153) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/Software/NeuroPedia/index.html

A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species.

Proper citation: NeuroPedia (RRID:SCR_001551) Copy   

•   Source: SciCrunch Registry

http://www.pd-doc.org/Databases/LinkedDatabases/PSGDatabases/ELLDOPAStudy/tabid/161/Default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from the ELLDOPA study: a multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial of 361 early, mild Parkinson's disease (PD) subjects, not requiring symptomatic medications with a duration from time of diagnosis less than 2 years. A NINDS funded study. The multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial, called the Earlier versus Later Levodopa Therapy in Parkinson Disease (ELLDOPA) study was run by the Parkinson Study Group and sponsored by the National Institute of Neurological Disorders and Stroke (NINDS). The subjects (n=361) were enrolled between September 1998 and August 2001 at 33 sites in the United States and 5 sites in Canada. Despite the known benefit of levodopa in reducing the symptoms of Parkinsons disease, concern has been expressed that its use might hasten neurodegeneration. This study assessed the effect of levodopa on the rate of progression of Parkinsons disease.The primary analysis assessed the doseresponse relationship between the assigned doses and the worsening of parkinsonism, as indicated by the changes in the total score on the UPDRS between the baseline visit and week 42. Washout of study drug occurred during weeks 40-42.

Proper citation: Earlier versus Later Levodopa Therapy in Parkinson Disease (RRID:SCR_001150) Copy   

•   Source: SciCrunch Registry