Technical reports (not peer-reviewed)

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    NCGAS 2021 Annual User Assessment Summary Report
    (2021-06-30) Jankowski, Harmony; Wernert, Julie; Sanders, Sheri
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    NCGAS 2020 Annual User Survey
    (2020-10-26) Wernert, Julie; Sanders, Sheri; Papudeshi, Bhavya; Jankowski, Harmony
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    NCGAS NSF Annual Report, September 1, 2019 – August 31, 2020
    (2020-09-09) Sanders, Sheri; Doak, Thomas; Snapp-Childs, Winona; Hahn, Matthew; Ye, Yuzhen; Stewart, Craig
    NCGAS annual report for project year 9.
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    ABI Sustaining: The National Center for Genome Analysis Support 2019 Annual Report
    (2019-09-10) Doak, Thomas; Stewart, Craig; Henschel, Robert; Ye, Yuzhen
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    Summary Report on Scaling the Introduction to R for Biologists Workshop by National Center for Genome Analysis Support (NCGAS) to a Massive Open Online Course (MOOC)
    (2019-12-10) Sanders, Sheri; Doak, Thomas; Ganote, Carrie; Papudeshi, Bhavya; Stewart, Craig
    The National Center For Genome Analysis Support successfully expanded the Introduction to R for Biologists Workshop from a locally offered, 30-person course to a full Massive Open Online Course. The course went through several iterations as an in-person course, then a hybrid course, in order to solidify materials (including Jetstream Cloud virtual machines) and record video lectures. This work was done in conjunction with several IU teams. We were able to show that teaching mode had no effect on learning outcomes, that participation and engagement did not suffer with an online course, and that instructor time was not largely impacted while scaling the course from 30 to 343 students. This course will continue to be offered in person locally (with reduced frequency) and in regular rotation as a MOOC, in order to meet the strong demand for basic coding skills in a domain-guided context.
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    Summary of the National Center for Genome Analysis Support (NCGAS) 2018-2019 de Novo Transcriptome Workflow and Workshops
    (2019-12-10) Sanders, Sheri; Doak, Thomas; Ganote, Carrie; Papudeshi, Bhavya; Stewart, Craig
    The National Center for Genome Analysis Support (NCGAS) has held a workshop entitled "de novo Assembly of Transcriptomes using HPC Resources" three times between April 2018 and May 2019. These workshops were in serving NCGAS's mission of enabling the biological research community to analyze, understand, and make use of the genomic information now available by packaging our now seven years of experience assisting with de novo transcriptome assemblies and running High Performance Computing (HPC) resources into a documented, easily approachable workflow for our users. The workshops covered common questions and problems that our users have had in HPC (such as job handling, resource availability, data management, and troubleshooting) and in the construction of transcriptomes (such as software choices, combination of assemblies, and downstream analyses). The three-day workshops also highlighted the available resources for US scientists, concentrating heavily on available XSEDE resources for analyses, visualization, and archiving of data.
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    NCGAS Annual User Assessment 2019 Summary Report
    (2019-09) Wernert, Julie A.; Jankowski, Harmony
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    ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report Stewart
    (2018-09-10) Doak, Thomas G.; Stewart, Craig A.; Michaels, Scott D.
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    Summary of annual NCGAS user survey (Summer 2018)
    (2018-09-10) Wernert, Julie; Doak, Thomas G.; Sanders, Sheri; Ganote, Carrie; Papudeshi, Bhavya
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    Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop
    (2018-06-07) Sanders, Sheri; Ganote, Carrie; Papudeshi, Bhavya; Stewart, Craig; Doak, Tom
    The National Center for Genome Analysis Support (NCGAS) held a workshop entitled "de novo Assembly of Transcriptomes using HPC Resources" on April 30th, 2018 through May 1, 2018. This workshop was in serving NCGAS's mission of enabling the biological research community to analyze, understand, and make use of the genomic information now available by packaging our now seven years of experience assisting with de novo transcriptome assemblies and running High Performance Computing (HPC) resources into a documented, easily approachable workflow for our users. The workshop covered common questions and problems that our users have had in HC (such as job handling, resource availability, data management, and troubleshooting) and in the construction of transcriptomes (such as software choices, combination of assemblies, and downstream analyses). The two-day workshop also highlighted the available resources for US scientists, concentrating heavily on available XSEDE resources for analyses, visualization, and archiving of data.
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    Summary of RT Survey of Field/Marine Station Director and Managers, Spring 2017
    (2017) Doak, Tom
    We hoped to gain a general perspective on the use and needs of stations for cyberinfrastructure, and further to assess their use of cloud resources, and willingness to adopt cloud resources, such as the NSF-funded Jetstream.This process was initiated by corresponding with colleagues in the field of ecology to gain a general idea of needs (see reply from David Inouye, Appendix 1) and by reviewing white papers and surveys by the National Association of Marine Laboratories and Organization of Biological Field Stations (NAML and OBFS; ref. 1-3).
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    Results of the 2014 Survey of NSF-funded researchers on their bioinformatics (genomics) needs
    (2014-12-31) Doak, Thomas G.; Barnett, William; Ganote, Carrie; Wu, Le-Shin
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    Summary of the 2017 NCGAS User Survey
    (2017-07-31) Doak, Thomas G.; Stewart, Craig A.; Michaels, Scott D.
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    ABI Sustaining: The National Center for Genome Analysis Support 2017 Annual Report
    (2017-06-30) Doak, Thomas G.; Stewart, Craig A.; Michaels, Scott D.
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    ABI Sustaining: The National Center for Genome Analysis Support 2016 Annual Report
    (2016-08-15) Doak, Thomas G.; Stewart, Craig A.; Michaels, Scott D.
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    ABI Development: National Center for Genome Analysis Support
    (2015-12-15) Stewart, Craig A.; Barnett, William K; Hahn, Matthew W.; Lynch, Michael R.
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    National Center for Genome Analysis Program Year 3 Report – September 15, 2013 – September 14, 2014
    (2014-08) Barnett, William K.; Stewart, Craig A.
    On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the third 12 months of NCGAS
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    National Center for Genome Analysis Program Year 2 Report – September 15, 2012 – September 14, 2013
    (2014-02-25) Barnett, William K.; LeDuc, Richard D.; Stewart, Craig A.
    On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the second 12 months of NCGAS
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    National Center for Genome Analysis Program Year 1 Report – September 15, 2011 – September 14, 2012
    (2013-03-04) Barnett, William; Ganote, Carrie; Vaughn, Matthew; LeDuc, Richard D.; Stewart, Craig A.
    On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the first 12 months of NCGAS, during which time NCGAS brought online a large-RAM computational cluster, recruited 25 NSF-funded genomics projects to use the resource, responded to 502 requests for support, and processed 28,523 computational jobs representing a total of 136.83 core years of computing. NCGAS also laid the framework for creating a truly national-scale center supporting genomics research. By coordinating effort between multiple supercomputing centers, NCGAS is creating a service-oriented computational infrastructure – one that is designed to be approachable by end-users unaccustomed to using traditional supercomputing resources. The benefits of such inter-institutional coordination can be seen from events such as the NCGAS co-hosted Daphnia Genomics Jamboree. At this gathering, dozens of scientists from across the US and Europe spent five days accelerating the completion of the Daphnia manga genome. NCGAS-supported staff from both Texas Advanced Computing Center (TACC) and IU gave presentations early in the Jamboree before participants broke into small teams and used NCGAS clusters to perform their analyses. NCGAS also established a Galaxy web portal to allow researchers to use our large-RAM cluster with a familiar web interface, and we worked to increase the computational efficiency of the best-in-class Trinity application for RNA-sequence assembly.