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https://code.google.com/p/ngsplot/

A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.

Proper citation: ngs.plot (RRID:SCR_011795) Copy   

•   Source: SciCrunch Registry

http://www.jalview.org/

A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.

Proper citation: Jalview (RRID:SCR_006459) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MetaQC/

Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision.

Proper citation: MetaQC (RRID:SCR_006000) Copy   

•   Source: SciCrunch Registry

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

Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans.

Proper citation: DIAMOND (RRID:SCR_009457) Copy   

•   Source: SciCrunch Registry

http://www.york.ac.uk/crd/

A research department of the University of York provides research-based information about the effects of health and social care interventions via their databases. The institute undertakes systematic reviews evaluating research evidence on health and public health questions of national and international importance.

Proper citation: Centre for Reviews and Dissemination (RRID:SCR_010267) Copy   

•   Source: SciCrunch Registry

http://www.biobase-international.com

THIS RESOURCE IS OUT OF SERVICE, documented on February 1st,2022. BIOBASE offers academic and non-profit organizations free access to TRANSFAC?? non-professional version with much reduced functionality and content compared to our professional database.

Proper citation: BIOBASE Corporation (RRID:SCR_010271) Copy   

•   Source: SciCrunch Registry

http://www.diogenes-eu.org

Diogenes is a pan-European Programme targeting the obesity problem from a dietary perspective: seeking new insights and new routes to prevention. An Integrated Project of the EU Sixth Framework Programme for Research and Technological Development (2005-2009). A new methodology has been developed for consistent assignment of GI values to foods across the five European databases used in the Diogenes intervention study. GI values have been assigned according to five decreasing levels of confidence: (1) Measured values for specific foods; (2) Published values from published sources; (3) Equivalent values where published values for similar foods existed; (4) Estimated values three values selected representing low/medium/high GI ranges; (5) Nominal values assigned as 70, where no other value could be assigned with sufficient confidence. Sponsor. A a r h u s K a r l s h a m n D e n m a r k A / S Products: Vegetable Oils (Maize and Rapeseed) click here for the link to the website of AarhusKarlshamn Denmark B a r i l l a Products: Pasta click here for the link to the website of Barilla B e a u v a i s Products: Canned fish products, jam, soups & convenience foods click here for the link to the website of Beauvais C a m p i n a I n s t i t u t e At the Campina Institute dairy products and science come together. The Campina brands include among others: Optimel/ Optiwel, Vifit, Milner, Valess Click here for the link to the website of Campina Institute C o c a - C o l a S e r v i c e s S . A . Products: beverages click here for the link to the website of Coca-Cola Services S.A. D a l o o n Products: Spring rolls and other convenience foods click here for the link to the website of Daloon D a n g S / A Products: egg products click here for the link to the website of Dang A/S D a n i s c o Products: Sugar (different types) click here for the link to the website of Danisco D a n i s h D a i r y B o a r d Products: Dairy products (milk, yoghurt, cheese) click here for the link to the website of the Danish Dairy Board D a n s k e S l a g t e r i e r Products: Pig Meat Products (various types) click here for the link to the website of Danske Slagterier D r . O e t k e r Products: Ready meals click here for the link to the website of Dr. Oetker E u r o g r a n A / S Products: Instant chocolate, cappuccino, soup and mashed poptatoes click here for the link to the website of Eurogran A/S F r i g o d a n Products: Frozen vegetables click here for the link to the website of Frigodan F r i s k o Products: Ice cream click here for the link to the website of Frisko G a m b a F o o d Products: Frozen fish (different types of European and Asian origin) G i l d e N o r g e B A Products: meat click here for the link to the website of Gilde Norge BA H a t t i n g Products: Bread products (different types) click here for the link to the website of Hatting H e i n z Products: ketchup and a broad range of products under HONIG, Konininklijke de Ruijter, VENZ, Carvan Cevitan, Roosvicee click here for the link to the website of Heinz H j e r t i n g L a k s Products: salmon products click here for the link to the website of Hjerting Laks K e l l o g g '' s D e n m a r k Products: different types of Breakfast Cereals Click here for the link to the website of Kellogg''s Denmark K e l l o g g '' s E u r o p e Products: Ready-To-Eat Cereals and Cereal Bars Click here for the link to the website of Kellogg''s K d b r a n c h e n s F l l e s r d Products: meat: beaf and veal click here for the link to the website of Kdbranchens Fllesrd K r a f t Products: chocolate, Philadelphia cream cheese, pasta, Estrella chips & nuts, mayonaise, salad dressings click here for the link to the website of Kraft L a n t m n n e n M i l l s A / S Products: various grains and flour L U , G e n e r a l B i s c u i t s N e d e r l a n d B . V . Products: biscuits click here for the link to the website of LU L y k k e b e r g A / S Products: Fish (marinated herring) click here for the link to the website of Lykkeberg A/S M a s t e r f o o d s Products: Rice and confectionery click here for the different websites of Masterfoods: Uncle Bens, Mars, Twix, Snickers, M&M''s, Masterfoods N u t r i t i o n e t S a n t / M o d i f a s t Products: Modifast (Low Calorie Diet) click here for the link to the website of Nutrition et Sant click here for the link to the website of Modifast P a r t n e r s h i p f o r D a n i s h P o t a t o e s Products: potatoes (different varieties) click here for the link to the website of the Partnership for Danish Potatoes P a s t a l i f e Products: pasta (with high protein content) click here for the link to the website of Pastalife R a h b e k Products: Frozen, ready-made fish dishes click here for the link to the website of Rahbek R i e b e r & S n D a n m a r k A / S Products: mustard, ketchup, mayonnaise, sanwich filling, spreads and other dressings click on the following links for the different websites of Rieber and Sn Danmark A/S: Rieberson, Bahncke, K-Salat R o y a l G r e e n l a n d A / S Products: cold-water prawns click here for the link to the website of Royal Greenlands A/S S c h u l s t a d Products: Rye bread and wheat bread, including high- and low GI varieties click here for the link to the website of Schulstad S n d e r j y d s k K l Products: Frozen kale, spinach and cabbage. click here for the link to the website of Snderjydsk Kl S u i k e r U n i e Products: different types of sugar click here for the link to the website of Suiker Unie T u l i p F o o d C o m p a n y Products: Meat products (cold cuts, cooked meat, bacon, meat balls, ready-meals, soups etc.) Click here for the link to the website of Tulip Food Company U n i l e v e r Products: a broad range of products under Becel, Bertolli, Calv, Knorr, Iglo, Mora, Conimex, Unox click here for the link to the website of Unilever W a s a b r d A / S Products: Crisp bread click on the following links for the different websites of Wasabrd A/S: Wasa Denmark or Wasa International

Proper citation: Diogenes (RRID:SCR_013293) Copy   

•   Source: SciCrunch Registry

http://www.atcc.org/

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

Proper citation: ATCC (RRID:SCR_001672) Copy   

•   Source: SciCrunch Registry

http://www.genoscope.cns.fr/spip/spip.php?lang=en

French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes.

Proper citation: Genoscope (RRID:SCR_002172) Copy   

•   Source: SciCrunch Registry

http://www.filemaker.com

A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline.

Proper citation: FileMaker (RRID:SCR_000783) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Proper citation: FastQ Screen (RRID:SCR_000141) Copy   

•   Source: SciCrunch Registry

http://www.brainbank.nl

A biomaterial supply resource which collects, stores, and disseminates diseased and healthy brain tissue. The Netherlands Brain Bank currently contains more than 3600 samples, and each sample includes a neuropathological report and donor medical history. The samples can additionally be matched with ante-mortem parameters and post-mortem parameters upon request. Sample types include cortex, spinal cord, cerebrospinal fluid, plasma, and DNA, among others. Database mining is available with a financial contribution.

Proper citation: Netherlands Brain Bank (RRID:SCR_013841) Copy   

•   Source: SciCrunch Registry

http://www.optibrium.com/stardrop/index.php

Software toolkit for drug design and discovery, including plugins for in silico compound optimization, compound selection and integration into other databases.

Proper citation: StarDrop (RRID:SCR_014902) Copy   

•   Source: SciCrunch Registry

http://www.alz.washington.edu/

A clinical research, neuropathological research and collaborative research database that uses data collected from 29 NIA-funded Alzheimer's Disease Centers (ADCs). The database consists of several datasets, and searches may be done on the entire database or on individual datasets. Any researcher, whether affiliated with an ADC or not, may request a data file for analysis or aggregate data tables. Requested aggregate data tables are produced and returned as soon as the queue allows (usually within 1-3 days depending on the complexity).

Proper citation: National Alzheimer's Coordinating Center (RRID:SCR_007327) Copy   

•   Source: SciCrunch Registry

http://www.mousephenotype.org/

Center that produces knockout mice and carries out high-throughput phenotyping of each line in order to determine function of every gene in mouse genome. These mice will be preserved in repositories and made available to scientific community representing valuable resource for basic scientific research as well as generating new models for human diseases.

Proper citation: International Mouse Phenotyping Consortium (IMPC) (RRID:SCR_006158) Copy   

•   Source: SciCrunch Registry

http://cerad.mc.duke.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Consortium that developed brief, standardized and reliable procedures for the evaluation and diagnosis of patients with Alzheimer's disease (AD) and other dementias of the elderly. These procedures included data forms, flipbooks, guidebooks, brochures, instruction manuals and demonstration tapes, which are now available for purchase. The CERAD assessment material can be used for research purposes as well as for patient care. CERAD has developed several basic standardized instruments, each consisting of brief forms designed to gather data on normal persons as well as on cognitively impaired or behaviorally disturbed individuals. Such data permit the identification of dementia based on clinical, neuropsychological, behavioral or neuropathological criteria. Staff at participating CERAD sites were trained and certified to administer the assessment instruments and to evaluate the subjects enrolled in the study. Cases and controls were evaluated at entry and annually thereafter including (when possible) autopsy examination of the brain to track the natural progression of AD and to obtain neuropathological confirmation of the clinical diagnosis. The CERAD database has become a major resource for research in Alzheimer's disease. It contains longitudinal data for periods as long as seven years on the natural progression of the disorder as well as information on clinical and neuropsychological changes and neuropathological manifestations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CERAD - Consortium to Establish a Registry for Alzheimer's Disease (RRID:SCR_003016) Copy   

•   Source: SciCrunch Registry

http://www.biomax.us/

Our robust searchable Tissue Bank database at US Biomax contains normal, non-cancerous disease and cancer samples, just a fraction of total paraffin tissue bank. Use advanced search function to define your search. Some of them have H&E images. Our tissue repository, tissue bank has huge paraffin tissue blocks, a large selection of histology tissue section slides of human cancer, normal tissue, rhesus and cynomolgus normal fresh frozen tissue as well as paraffin blocks and slides. It has also normal human organs in paraffin embedded tissue blocks as well as rhesus and cynomolgus monkey normal organ tissues. Snap frozen (fresh frozen) tissue of rhesus/cynomolgus monkey are also available. We also provide tissue array, custom tissue microarray (with samples you provided or from our tissue bank) as well as OEM services. Other products/services available include tissue microarray, paraffin tissue sections, histology services and quantitative telomerase detection kit.

Proper citation: US Biomax (RRID:SCR_004295) Copy   

•   Source: SciCrunch Registry

http://dbmi.mc.vanderbilt.edu/research/dnadatabank.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. BioVU is a research resource providing a View into biology at the level of DNA and other important macromolecules. BioVU has two major components. The first is a repository of DNA samples (extracted from discarded blood samples) that are coded solely by a Research Unique Identifier (RUI) derived from the Medical Record Number (MRN) using a one-way hash function. This is a computer algorithm that creates a transformation of each MRN such that the resulting RUI (which is in this instance is a 512 byte identifier) is unique, and has the property that it is not possible to infer or compute the MRN that generated it. As of early 2009, over 50,000 DNA samples were in the biobank, with new samples being added at the rate of approximately 700 per week. The second component of the resource is the creation of a database known as the Synthetic Derivative which is a collection of de-identified information extracted from VUMC''s electronic clinical information systems, indexed by the same one-way RUI used to track samples, and with content changed by deletion or permutation of all identifiers contained within each record. The Synthetic Derivative search interface is available to Vanderbilt researchers via the StarBRITE research portal created and maintained by the Vanderbilt Institute for Clinical and Translational Research. This user interface enables investigators meeting protocol approval criteria and other user agreement requirements to receive protocol-specific sets of data derived from DNA samples and from the Synthetic Derivative., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Vanderbilt BioVU (RRID:SCR_004632) Copy   

•   Source: SciCrunch Registry

http://www.genmapp.org/

GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options.

Proper citation: Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) Copy   

•   Source: SciCrunch Registry

http://pubmatrix.grc.nia.nih.gov/

PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence. PubMatrix is a simple way to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. Lists of terms can be anything; gene names, diseases, gene functions, authors, etc. The user can then quickly sort or browse the frequency matrix table to do individual searches independently. This allows the user to build up tables of word relationships in PubMed in the context of your experiments or your scientific interests. This is useful for analyzing combinatorial datasets, as found with multiplex experimental systems, such as cDNA microarrays, genomic, proteomic, or other multiplex comparisons. The PubMatrix database is an archive of previous searches on many topics. Sponsors: PubMatrix is supported by the National Institutes of Health.

Proper citation: PubMatrix (RRID:SCR_008236) Copy   

•   Source: SciCrunch Registry