2024-03-28T15:32:54Zhttps://scholarworks.iu.edu/dspace-oai/requestoai:scholarworks.iu.edu:2022/153402021-10-18T12:07:22Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Barnett, William
author
Ganote, Carrie
author
Vaughn, Matthew
author
LeDuc, Richard D.
author
Stewart, Craig A.
author
3/4/2013
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.
http://hdl.handle.net/2022/15340
NCGAS
National Center for Genome Analysis Support
National Center for Genome Analysis Program Year 1 Report – September 15, 2011 – September 14, 2012
oai:scholarworks.iu.edu:2022/173872021-10-18T10:45:05Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Barnett, William K.
author
LeDuc, Richard D.
author
Stewart, Craig A.
author
2/25/2014
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
Barnett, W.K., LeDuc, R.D., and Stewart, C.A. “National Center for Genome Analysis Program Year 2 Report – September 15, 2012 – September 14, 2013.” Indiana University, Bloomington, IN. PTI Technical Report PTI-TR14-004, 2014.
http://hdl.handle.net/2022/17387
NCGAS, genomics, Stampede, Blacklight, Dublin Core metadata, transcriptome- and genome-level assembly, phylogenetics, metagenomics/transcriptomics, community genomics, consulting, XSEDE, Rockhopper, Mason,
National Center for Genome Analysis Program Year 2 Report – September 15, 2012 – September 14, 2013
oai:scholarworks.iu.edu:2022/185132021-10-18T15:05:56Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Barnett, William K.
author
Stewart, Craig A.
author
2014-08
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
http://hdl.handle.net/2022/18513
NCGAS, genomics, Stampede, Blacklight, Dublin Core metadata, transcriptome- and genome-level assembly, phylogenetics, metagenomics/transcriptomics, community genomics, consulting, XSEDE, Rockhopper, Mason,
National Center for Genome Analysis Program Year 3 Report – September 15, 2013 – September 14, 2014
oai:scholarworks.iu.edu:2022/207412021-10-18T12:54:03Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Stewart, Craig A.
author
Barnett, William K
author
Hahn, Matthew W.
author
Lynch, Michael R.
author
2015-12-15
Stewart, S.A., Barnett, W.K., Hahn, M.W., and Lynch, M.R. “ABI development: National center for genome analysis support”, Indiana University, Bloomington, IN. PTI Technical Report PTI-TR15-009, Dec 2015.
http://hdl.handle.net/2022/20741
ABI Development: National Center for Genome Analysis Support
oai:scholarworks.iu.edu:2022/209572021-10-18T10:59:55Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Doak, Thomas G.
author
Stewart, Craig A.
author
Michaels, Scott D.
author
2016-08-15
http://hdl.handle.net/2022/20957
ABI Sustaining: The National Center for Genome Analysis Support 2016 Annual Report
oai:scholarworks.iu.edu:2022/216132021-10-18T15:07:03Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Doak, Thomas G.
author
Stewart, Craig A.
author
Michaels, Scott D.
author
2017-06-30
Doak, T.G., Stewart, C.A., Michaels, S.D. (2017) “ABI development: National center for genome analysis support 2017 annual report”, Indiana University, Bloomington, IN. PTI Technical Report PTI-TR17-003. Retrieved from http://hdl.handle.net/2022/21613
http://hdl.handle.net/2022/21613
ABI Sustaining: The National Center for Genome Analysis Support 2017 Annual Report
oai:scholarworks.iu.edu:2022/216142021-10-18T15:06:55Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Doak, Thomas G.
author
Stewart, Craig A.
author
Michaels, Scott D.
author
2017-07-31
Doak, T.G., Stewart, C.A., Michaels, S.D. (2017) “Summary of the 2017 NCGAS User Survey”, Indiana University, Bloomington, IN. PTI Technical Report PTI-TR17- 005. Retrieved from http://hdl.handle.net/2022/21614
http://hdl.handle.net/2022/21614
Summary of the 2017 NCGAS User Survey
oai:scholarworks.iu.edu:2022/216222021-10-18T15:43:22Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Doak, Thomas G.
author
Barnett, William
author
Ganote, Carrie
author
Wu, Le-Shin
author
2014-12-31
Doak, T.G., Barnett, W., Ganote, C., & Wu, L.S. (2014) “Results of the 2014 Survey of NSF-funded researchers on their bioinformatics (genomics) needs”, Indiana University, Bloomington, IN. PTI Technical Report PTI-TR14-015. Retrieved from http://hdl.handle.net/2022/21622
http://hdl.handle.net/2022/21622
Results of the 2014 Survey of NSF-funded researchers on their bioinformatics (genomics) needs
oai:scholarworks.iu.edu:2022/220092018-04-04T20:15:10Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Doak, Tom
author
2017
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).
Doak, T.G. (2017) “Summary of RT Survey of Field/Marine Station Director and Managers, Spring 2017”, Indiana University, Bloomington, IN. PTI Technical Report. Retrieved from http://hdl.handle.net/2022/22009
http://hdl.handle.net/2022/22009
Field Station
NCGAS
Survey
Summary of RT Survey of Field/Marine Station Director and Managers, Spring 2017
oai:scholarworks.iu.edu:2022/222542021-10-19T03:41:41Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Sanders, Sheri
author
Ganote, Carrie
author
Papudeshi, Bhavya
author
Stewart, Craig
author
Doak, Tom
author
2018-06-07
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.
Sanders, S., C. Ganote, B. Papudeshi, C. Stewart. T. Doak. (2018) “Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop”, Indiana University, Bloomington, IN. PTI Technical Report. Retrieved from http://hdl.handle.net/2022/22254
http://hdl.handle.net/2022/22254
NCGAS
Workshop
NSF Report
Transcriptome Assembly
Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop
oai:scholarworks.iu.edu:2022/224012018-10-10T15:15:38Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Wernert, Julie
author
Doak, Thomas G.
author
Sanders, Sheri
author
Ganote, Carrie
author
Papudeshi, Bhavya
author
2018-09-10
Wernert, J., Doak, T.G., Sanders, S., Ganote, C. & Pallipapudesh, B. (2018). Summary of the annual NCGAS user survey (Summer 2018).
http://hdl.handle.net/2022/22401
NCGAS, user survey, satisfaction
Summary of annual NCGAS user survey (Summer 2018)
oai:scholarworks.iu.edu:2022/224022021-10-18T16:55:46Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Doak, Thomas G.
author
Stewart, Craig A.
author
Michaels, Scott D.
author
2018-09-10
Doak, T. G., Stewart, C. A., & Michaels, S. D. (2018). ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report (PTI Technical Report PTI-TR18-004). Indiana University, Bloomington, IN. Retrieved from http://hdl.handle.net/2022/22402
http://hdl.handle.net/2022/22402
NCGAS, National Science Foundation
ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report Stewart
oai:scholarworks.iu.edu:2022/236292021-10-18T17:57:14Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Wernert, Julie A.
author
Jankowski, Harmony
author
2019-09
http://hdl.handle.net/2022/23629
annual user assessment, user support, genomics
NCGAS Annual User Assessment 2019 Summary Report
oai:scholarworks.iu.edu:2022/248872021-10-19T04:47:24Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Sanders, Sheri
author
Doak, Thomas
author
Ganote, Carrie
author
Papudeshi, Bhavya
author
Stewart, Craig
author
2019-12-10
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.
Sanders, S., C. Ganote, B. Papudeshi, C. Stewart. T. Doak. (2019) “Summary of the National Center for Genome Analysis Support (NCGAS) 2018-2019 de Novo Transcriptome Workflow and Workshops”, Indiana University, Bloomington, IN. PTI Technical Report. Retrieved from http://hdl.handle.net/2022/24887
http://hdl.handle.net/2022/24887
NCGAS
Workshop Design
Summary of the National Center for Genome Analysis Support (NCGAS) 2018-2019 de Novo Transcriptome Workflow and Workshops
oai:scholarworks.iu.edu:2022/248882021-10-19T04:47:26Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Sanders, Sheri
author
Doak, Thomas
author
Ganote, Carrie
author
Papudeshi, Bhavya
author
Stewart, Craig
author
2019-12-10
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.
Sanders, S., C. Ganote, B. Papudeshi, C. Stewart. T. Doak. (2019) "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)", Indiana University, Bloomington, IN. PTI Technical Report. Retrieved from http://hdl.handle.net/2022/24888
http://hdl.handle.net/2022/24888
NCGAS
Workshop Design
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)
oai:scholarworks.iu.edu:2022/251332021-10-18T12:10:42Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Doak, Thomas
author
Stewart, Craig
author
Henschel, Robert
author
Ye, Yuzhen
author
2019-09-10
Doak, T. G., Stewart, C. A., Henschel, R., Yuzhen, Y. (2019). ABI Sustaining: The National Center for Genome Analysis Support 2019 Annual Report (PTI Technical Report). Indiana University, Bloomington, IN. Retrieved from http://hdl.handle.net/2022/25133.
http://hdl.handle.net/2022/25133
NCGAS
PTI
Annual Report
Genomics
ABI Sustaining: The National Center for Genome Analysis Support 2019 Annual Report
oai:scholarworks.iu.edu:2022/258772021-10-19T00:57:17Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Sanders, Sheri
author
Doak, Thomas
author
Snapp-Childs, Winona
author
Hahn, Matthew
author
Ye, Yuzhen
author
Stewart, Craig
author
2020-09-09
NCGAS annual report for project year 9.
Sanders, S., Snapp-Childs, W., Doak, T. G., Stewart, C. A., Yuzhen, Y. (2019). NCGAS NSF Annual Report; September 1,2019 through August 31, 2020 (PTI Technical Report). Indiana University, Bloomington, IN. Retrieved from .
http://hdl.handle.net/2022/25877
Annual Report
NCGAS
PTI
NCGAS NSF Annual Report, September 1, 2019 – August 31, 2020
oai:scholarworks.iu.edu:2022/258782021-10-19T00:53:33Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Wernert, Julie
author
Sanders, Sheri
author
Papudeshi, Bhavya
author
Jankowski, Harmony
author
2020-10-26
http://hdl.handle.net/2022/25878
NCGAS 2020 Annual User Survey
oai:scholarworks.iu.edu:2022/266262021-10-19T05:06:03Zcom_2022_14531com_2022_356com_2022_19673col_2022_14535
00925njm 22002777a 4500
dc
Jankowski, Harmony
author
Wernert, Julie
author
Sanders, Sheri
author
2021-06-30
http://hdl.handle.net/2022/26626
NCGAS, user survey, satisfaction
NCGAS 2021 Annual User Assessment Summary Report