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http://www.ncbi.nlm.nih.gov/books/NBK25500/

Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.
Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course.
User Requirements: Please read for important information on scripting NCBI servers.
EInfo: Provides field index term counts, last update, and available links for each database.
ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment.
EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies.
ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment.
EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment.
ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs.
EGQuery: Provides Entrez database counts in XML for a single search using Global Query.
ESpell: Retrieves spelling suggestions.
SOAP Interface for Entrez Utilities
PMID to PMC ID Converter
Entrez DTDs
Demonstration Program
Announcement Mailing List
Leasing Data from the National Library of Medicine
Help Desk
User Requirements
Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following:
Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests.
Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address.
Make no more than 3 requests every 1 second.
Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem.
NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.

Proper citation: Entrez Utilities (RRID:SCR_013249) Copy   

•   Source: SciCrunch Registry

http://www.softpedia.com/get/Science-CAD/BrainVisa-Morphology-extensions.shtml

An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa

Proper citation: BrainVisa Morphology extensions (RRID:SCR_013248) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirseq/files/

An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

Proper citation: miRSeqNovel (RRID:SCR_013257) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ligmap/files/

A tool for structural biology and drug design.

Proper citation: AutoMap (RRID:SCR_013095) Copy   

•   Source: SciCrunch Registry

http://www.usphs.gov/

Commissioned Corps of the United States Public Health Service, is the federal uniformed service of the U.S. Public Health Service, and is one of the eight uniformed services of the United States.

Proper citation: U.S. Public Health Service Commissioned Corps (RRID:SCR_013104) Copy   

•   Source: SciCrunch Registry

http://beads.sourceforge.net/

Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.

Proper citation: BEADS (RRID:SCR_013229) Copy   

•   Source: SciCrunch Registry

http://www.lifetechnologies.com/fr/fr/home/technical-resources/software-downloads/lifescope-genomic-analysis-software.html

Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC).

Proper citation: LifeScope (RRID:SCR_013234) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/congrpe/

A de novo assembly algorithm for Next-Generation Sequencing technology.

Proper citation: CongrPE (RRID:SCR_013190) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sapas/

A RNA-seq method for polyA research.

Proper citation: SAPAS (RRID:SCR_013195) Copy   

•   Source: SciCrunch Registry

http://derisilab.ucsf.edu/index.php?software=105

An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets.

Proper citation: HMMSplicer (RRID:SCR_013315) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.

Proper citation: Trans-ABySS (RRID:SCR_013322) Copy   

•   Source: SciCrunch Registry

http://neuma.kobic.re.kr/

Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data.

Proper citation: NEUMA (RRID:SCR_013324) Copy   

•   Source: SciCrunch Registry

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

Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data.

Proper citation: chimerascan (RRID:SCR_013298) Copy   

•   Source: SciCrunch Registry

http://waprna.big.ac.cn/

A free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of Applied Biosystems (SOLiD).

Proper citation: wapRNA (RRID:SCR_013292) 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.chadd.org/

Non-profit organization serving individuals with attention deficit-hyperactivity disorder (AD/HD) and their families. CHADD has over 16,000 members in 200 local chapters throughout the U.S. Chapters offer support for individuals, parents, teachers, professionals, and others. CHADD''s primary objectives are: to provide a support network for parents and caregivers; to provide a forum for continuing education; to be a community resource and disseminate accurate, evidence-based information about AD/HD to parents, educators, adults, professionals, and the media; to promote ongoing research; and to be an advocate on behalf of the AD/HD community. In general, CHADD works to improve the lives of people affected by AD/HD through: Collaborative Leadership, Advocacy, Research Education and, Support CHADD has three current priority objectives: (1) to serve as a clearinghouse for evidence-based information on AD/HD, (2) to serve as a local face-to-face family support group for families and individuals affected by AD/HD, and (3) to serve as an advocate for appropriate public policies and public recognition in response to needs faced by families and individuals with AD/HD. CHADD is a membership organization, produces the bi-monthly Attention! magazine (for members), and sponsors an annual conference. The National Resource Center on AD/HD (NRC) is the CDC-funded national clearinghouse for evidence-based information about AD/HD.

Proper citation: Children and Adults with Attention Deficit/Hyperactivity Disorder (RRID:SCR_013384) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/

Medical school of the University of Pennsylvania. It is located in the University City section of Philadelphia.

Proper citation: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA (RRID:SCR_013302) Copy   

•   Source: SciCrunch Registry

https://www.mabtech.com/

An Antibody supplier

Proper citation: MABTECH (RRID:SCR_013398) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/Pharmacology/dcpr95.html

These programs have been written over the last 20 years for analysis of our own results. They all do some things that are still not available in any commercial program. The programs are written in protected-mode 32-bit Fortran 90, with some assembler subroutines for fast graphics, and the Gino graphics library. Thus they are essentially DOS programs, though they are usually run from Windows, either via a desktop icon (the .ico files) or in the DOS box. The manuals (now in pdf format), have now all been collected into a single document, DCMANUALS.PDF, which should be downloaded, and the bits that you need can then be printed. Note that some sections are common to many or all programs, e.g. the notes on the graph and histogram drawing subroutines, and it is important to read this before using any of the programs (though there is a lot of online help (hit F1) for the graphics, and also in SCAN. Sponsor. Our work was supported by the Wellcome Trust (project grant 074491) and the Medical Research Council (programme grant G0400869).

Proper citation: DC Analysis programs (RRID:SCR_013431) Copy   

•   Source: SciCrunch Registry

http://graylab.jhu.edu/docking/rosetta/

Predicts the structure of a protein-protein complex from the individual structures of the monomer components.

Proper citation: RosettaDock (RRID:SCR_013393) Copy   

•   Source: SciCrunch Registry