scholarly journals Introduction to Genomic Analysis Workshop: A catalyst for engaging life-science researchers in high throughput analysis

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1221 ◽  
Author(s):  
Phillip A. Richmond ◽  
Wyeth W. Wasserman

Researchers in the life sciences are increasingly faced with the task of obtaining compute resources and training to analyze large, high-throughput technology generated datasets. As demand for compute resources has grown, high performance computing (HPC) systems have been implemented by research organizations and international consortiums to support academic researchers. However, life science researchers lack effective time-of-need training resources for utilization of these systems. Current training options have drawbacks that inhibit the effective training of researchers without experience in computational analysis. We identified the need for flexible, centrally-organized, easily accessible, interactive, and compute resource specific training for academic HPC use.  In our delivery of a modular workshop series, we provided foundational training to a group of researchers in a coordinated manner, allowing them to further pursue additional training and analysis on compute resources available to them. Efficacy measures indicate that the material was effectively delivered to a broad audience in a short time period, including both virtual and on-site students. The practical approach to catalyze academic HPC use is amenable to diverse systems worldwide.

2018 ◽  
Author(s):  
Phillip Andrew Richmond ◽  
Wyeth W Wasserman

Researchers in the life sciences are increasingly faced with the task of obtaining compute resources and training to analyze large, high-throughput technology generated datasets. As demand for compute resources has grown, high performance computing (HPC) systems have been implemented by research organizations and international consortiums to support academic researchers. However, life science researchers lack effective time-of-need training resources for utilization of these systems. Current training options have drawbacks that inhibit the effective training of researchers without experience in computational analysis. We identified the need for flexible, centrally-organized, easily accessible, interactive, and compute resource specific training for academic HPC use. In our delivery of a modular workshop series, we provided foundational training to a group of researchers in a coordinated manner, allowing them to further pursue additional training and analysis on compute resources available to them. Efficacy measures indicate that the material was effectively delivered to a broad audience in a short time period, including both virtual and on-site students. The practical approach to catalyze academic HPC use is amenable to diverse systems worldwide.


2003 ◽  
Vol 8 (2) ◽  
pp. 210-215 ◽  
Author(s):  
Barbara A. Kozikowski ◽  
Thomas M. Burt ◽  
Debra A. Tirey ◽  
Lisa E. Williams ◽  
Barbara R. Kuzmak ◽  
...  

A diverse set of 320 compounds from the Procter & Gamble Pharmaceuticals organic compound repository was prepared as 20-mM DMSO solutions and stored at 4°C under argon in pressurized canisters to simulate a low-humidity environment. The plates were subjected to 25 freeze/thaw cycles while being exposed to ambient atmospheric conditions after each thaw to simulate the time and manner by which compound plates are exposed to the atmosphere during typical liquid-handling and high-throughput screening processes. High-performance liquid chromatography–mass spectrometry with evaporative light-scattering detection was used to quantitate the amount of compound remaining after every 5th freeze/thaw cycle. Control plates were stored either at room temperature under argon or at 4°C under argon without freeze/thaw cycling and were evaluated at the midpoint and the endpoint of the study. The study was conducted over a short time period (i.e., 7 weeks) to minimize the effect of compound degradation over time due to the exposure of the compounds to DMSO.The results from this study will be used to determine the maximum number of freeze/thaw cycles that can be achieved while maintaining acceptable compound integrity.(Journal of Biomolecular Screening 2003:210-215)


2005 ◽  
Vol 47 (6) ◽  
Author(s):  
Ralf Reinhardt ◽  
Martin Blüggel ◽  
Christian Stephan ◽  
Helmut E. Meyer ◽  
Michael Kuhn ◽  
...  

ZusammenfassungObwohl man Cluster erfolgreich für Aufgaben wie Protein Identifikation und multiple alignment einsetzt, sind sie dennoch selten Teil des Laboralltags. Hauptgrund ist die schlechte Integrationsfähigkeit aktueller Lösungen in den Arbeitsablauf. Das Konzept Dienste Orientierter Cluster soll dieses Problem beheben.


2005 ◽  
Vol 1073 (1-2) ◽  
pp. 17-23 ◽  
Author(s):  
Yukihiro Shintani ◽  
Keiji Hirako ◽  
Masanori Motokawa ◽  
Takeshi Iwano ◽  
Xiaojing Zhou ◽  
...  

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