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DIAG Wiki

Welcome to the DIAG Wiki. If encounter any problems, or require assistance with how to perform a specific task, you should start by checking here for help and documentation. We also encourage you to improve the documentation yourself if you feel it is incomplete or unclear. If you are unable to find an answer to your question or are still experiencing problems, please let us know by Reporting a problem. Nimbus and Cloud Client. Nimbus and Amazon EC2 tools. This page has been accessed 115,919 times.

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Welcome to the DIAG Wiki. If encounter any problems, or require assistance with how to perform a specific task, you should start by checking here for help and documentation. We also encourage you to improve the documentation yourself if you feel it is incomplete or unclear. If you are unable to find an answer to your question or are still experiencing problems, please let us know by Reporting a problem. Nimbus and Cloud Client. Nimbus and Amazon EC2 tools. This page has been accessed 115,919 times.
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DIAG Wiki | wiki.diagcomputing.org Reviews

https://wiki.diagcomputing.org

Welcome to the DIAG Wiki. If encounter any problems, or require assistance with how to perform a specific task, you should start by checking here for help and documentation. We also encourage you to improve the documentation yourself if you feel it is incomplete or unclear. If you are unable to find an answer to your question or are still experiencing problems, please let us know by Reporting a problem. Nimbus and Cloud Client. Nimbus and Amazon EC2 tools. This page has been accessed 115,919 times.

INTERNAL PAGES

wiki.diagcomputing.org wiki.diagcomputing.org
1

Changes related to "Main Page" - DIAG Wiki

http://wiki.diagcomputing.org/index.php/Special:RecentChangesLinked/Main_Page

Changes related to "Main Page". This is a list of changes made recently to pages linked from a specified page (or to members of a specified category). Pages on your watchlist. This edit created a new page (also see list of new pages. This is a minor edit. This edit was performed by a bot. The page size changed by this number of bytes. Changes in last 1. Show new changes starting from 10:26, 18 September 2016. Show changes to pages linked to the given page instead.

2

Recent changes - DIAG Wiki

http://wiki.diagcomputing.org/index.php/Special:RecentChanges

Track the most recent changes to the wiki on this page. This edit created a new page (also see list of new pages. This is a minor edit. This edit was performed by a bot. The page size changed by this number of bytes. Changes in last 1. Show new changes starting from 10:26, 18 September 2016. No changes during the given period matching these criteria. Retrieved from " http:/ wiki.diagcomputing.org/index.php/Special:RecentChanges.

3

Ergatis - DIAG Wiki

http://wiki.diagcomputing.org/index.php/Ergatis

Accessing Ergatis on DIAG. Creating a project area. Launching an Ergatis pipeline. Screenshot of the Ergatis pipeline monitor. Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence M...Use the l...

4

Sun Grid Engine - DIAG Wiki

http://wiki.diagcomputing.org/index.php/Sun_Grid_Engine

DIAG has a computational grid that is used for scheduling, distributing, and monitoring jobs. The scheduler in use is Sun Grid Engine (SGE), which was a Sun Microsystems product and then acquired by Oracle in 2008. For those who wish to read more about Sun Grid Engine, the product page is located here. Submitting a batch job. Submitting an "array" job. Submitting a multi-threaded job. Submitting an interactive job. Retrieved from " http:/ wiki.diagcomputing.org/index.php?

5

File system layout - DIAG Wiki

http://wiki.diagcomputing.org/index.php/File_system_layout

All accounts are provided a home directory so that the user may configure their environment, install scripts, and store files they are actively working on. Home directories are dedicated to the user. A quota is configured on all home directories. On DIAG, all user home directories are stored under the /diag/home. Directory and are named after the user's username. For example, if the user's username is diaguser. Then the home directory would be /diag/home/diaguser. Is replaced with the actual username.

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LINKS TO THIS WEBSITE

diagcomputing.org diagcomputing.org

DIAG - Projects

http://www.diagcomputing.org/about/projects.php

Login not recognized, please retry. Login not recognized, please retry. DIAG is an important component of several bioinformatics related research projects. DIAG is currently providing computational resources for several bioinformatics software development projects, analysis efforts, and other initiatives that require large scale and highly performant compute resources and storage. Some of these are detailed below. In addition, the manual annotation tool Manatee.

diagcomputing.org diagcomputing.org

DIAG - Funding

http://www.diagcomputing.org/about/funding.php

Login not recognized, please retry. Login not recognized, please retry. Large-scale analysis has now become an integral part of nearly all research areas in biology. Institute for Genome Sciences. Lawrence Berkeley National Laboratory. University of Virginia School of Medicine. This project is supported by the National Science Foundation under Grant No. 0959894 titled MRI-R2: Acquisition of Data Intensive Academic Grid (DIAG).

diagcomputing.org diagcomputing.org

DIAG - Software

http://www.diagcomputing.org/resources/software.php

Login not recognized, please retry. Login not recognized, please retry. DIAG offers a wide range of bioinformatics tools to help researchers in their studies. National Center for Biotechnology Information. HMMER by HHMI Janelia Farm. Johns Hopkins Bloomberg School of Public Health.

diagcomputing.org diagcomputing.org

DIAG - DIAG User Community

http://www.diagcomputing.org/about/community.php

Login not recognized, please retry. Login not recognized, please retry. The DIAG user community is a diverse group of individuals from a variety of backgrounds. This community spans the globe, as visible in the map below.

diagcomputing.org diagcomputing.org

DIAG - Ergatis

http://www.diagcomputing.org/ergatis

Login not recognized, please retry. Login not recognized, please retry. Ergatis is a web based system for creating, modifying and executing bioinformatics pipelines. Ergatis Project at Sourceforge. Because of its flexibility, scalability, and ease-of-use, Ergatis has been an important part of the annotation of several large, eukaryotic organisms, including Aedes aegypti. Without concerning themselves with installation and configuration issues. Page We will notify you when the system is available for use.

diagcomputing.org diagcomputing.org

DIAG - Hardware

http://www.diagcomputing.org/resources/hardware.php

Login not recognized, please retry. Login not recognized, please retry. DIAG offers a wide range of bioinformatics tools to help researchers in their studies. National Center for Biotechnology Information. HMMER by HHMI Janelia Farm. Johns Hopkins Bloomberg School of Public Health. Data Intensive Academic Grid (DIAG) is a hybrid infrastructure setup as a shared resource for the bioinformatics community. 125 Dual-Processor (Intel Westmere six core) nodes. 48 GB RAM per node. 35 TB local storage per node.

diagcomputing.org diagcomputing.org

DIAG - Password Reset

http://www.diagcomputing.org/internal/reset.php

Login not recognized, please retry. Login not recognized, please retry. If you have lost or would like to reset your current password, please enter your DIAG username or email address below. Username or email address.

diagcomputing.org diagcomputing.org

DIAG - Investigators

http://www.diagcomputing.org/about/investigators.php

Login not recognized, please retry. Login not recognized, please retry. Large-scale analysis has now become an integral part of nearly all research areas in biology. Institute for Genome Sciences. Lawrence Berkeley National Laboratory. University of Virginia School of Medicine. Owen White, Ph.D. Principal Investigator. Owen R. White is the Director of the Bioinformatics department at the Institute for Genome Sciences (IGS). In Baltimore, Maryland. Samuel Angiuoli, Ph.D. Co-Principal Investigator. Anup ha...

diagcomputing.org diagcomputing.org

DIAG - News

http://www.diagcomputing.org/news/news.php

Login not recognized, please retry. Login not recognized, please retry. Large-scale analysis has now become an integral part of nearly all research areas in biology. Institute for Genome Sciences. DIAG presented at AGBT 2012. DIAG presented at Genome Informatics 2011. CloVR and DIAG presented at ISMB/ECCB 2011. Whole Genome Sequence Data for German E. Coli Outbreak Strain. An international team of experts on E. coli collaborated on the rapid sequencing project. MORE.

diagcomputing.org diagcomputing.org

DIAG - Citation

http://www.diagcomputing.org/support/citation.php

Login not recognized, please retry. Login not recognized, please retry. If you used DIAG and cited it in a publication, we would appreciate hearing about it. Use the form below to reference the publication, either by using the PubMed ID or by manually entering the journal/periodical name, date published, and title of the article. To cite DIAG in your publication, please use the text in the following form: "This research was conducted on the National Science Foundation funded MRI-R2 project #DBI-0959894".

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DIAG Wiki

Welcome to the DIAG Wiki. If encounter any problems, or require assistance with how to perform a specific task, you should start by checking here for help and documentation. We also encourage you to improve the documentation yourself if you feel it is incomplete or unclear. If you are unable to find an answer to your question or are still experiencing problems, please let us know by Reporting a problem. Nimbus and Cloud Client. Nimbus and Amazon EC2 tools. This page has been accessed 115,919 times.

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