User talk:Kam D. Dahlquist: Difference between revisions
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What | *What methods do you use in researching "The Global Transcriptional Response of Saccharomyces cerevisiae to Cold Shock and Recovery"? [[User:Lauren M. Kelly|Lauren M. Kelly]] 16:13, 15 January 2017 (EST) | ||
** We use a technology called DNA microarrays that can measure the expression of all the genes in yeast at once. We will be learning about this in the second half of the semester. ''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:53, 18 January 2017 (EST)'' | |||
*Will the Bioremediation processes being studied on the Ballona Wetlands be affective in different soil types across the world?*'''[[User:Cameron M. Rehmani Seraji|Cameron M. Rehmani Seraji]] 23:55, 16 January 2017 (EST)''': | |||
** That's not really my area of expertise. My project in the wetlands was sampling soil bacteria and identifying them by their 16S rRNA sequence tags. If phytoremediation is used, i.e., plants are grown to suck up the contaminants and then harvested to discard, it would work as long as the plant could grow there. Dr. Drennan is more of an expert on this than me. ''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:56, 18 January 2017 (EST)'' | |||
*What influenced you to embrace the mathematical side of biology? Was it a specific person? Research you came across? [[User:Conor Keith|Conor Keith]] 00:07, 18 January 2017 (EST) | |||
** I started when I was a postdoc and realized that statistics were required to analyze the microarray data that I was working with. I started the modeling project when I came to LMU because I wanted to understand the gene regulatory networks I was studying at a deeper level. So I really got interested in math to use as a tool to answer the biological questions I had. ''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 20:01, 18 January 2017 (EST)'' | |||
If | *What prompted you and Dondi to create the XMLPipeDB and what sparked your interest in expanding the amount of open source software available? [[User:Margaret J. Oneil|Margaret J. Oneil]] 00:22, 19 January 2017 (EST) | ||
** We started XMLPipeDB to solve a problem that GenMAPP was having, i.e., it was difficult to update or create new Gene Databases so that it could be used to analyze those species' data. At the time we started, the computer science professors had an NSF grant to bring open source development into their undergraduate curriculum and I had been frustrated as a postdoc because GenMAPP did not start out as being open source. When Dr. Dionisio explained to me the other facets of open source culture, besides the license, I was in. The rest, as they say, is history. ''‐ [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 02:17, 24 January 2017 (EST)'' | |||
*Prior to starting the modeling project at LMU had you ever been introduced to a similar project during your education that helped shape the current project? *'''[[User:Nika Vafadari|Nika Vafadari]] 02:34, 19 January 2017 (EST)''': | |||
** During my postdoc, I had previously worked on analyzing DNA microarray data by visualizing the data on pathways, but it didn't involve modeling, just statistics, and we were not studying gene regulatory pathways, mainly metabolic pathways. My interest in systems biology and gene regulatory networks was inspired, in part, by reading books on my own, especially those by Stuart Kauffman of the Santa Fe Institute (a research institute for complex systems). I attended a talk he gave at UC Santa Cruz, which must have been 20 years ago now. ''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 02:44, 24 January 2017 (EST)'' | |||
Revision as of 00:44, 24 January 2017
- What methods do you use in researching "The Global Transcriptional Response of Saccharomyces cerevisiae to Cold Shock and Recovery"? Lauren M. Kelly 16:13, 15 January 2017 (EST)
- We use a technology called DNA microarrays that can measure the expression of all the genes in yeast at once. We will be learning about this in the second half of the semester. — Kam D. Dahlquist 19:53, 18 January 2017 (EST)
- Will the Bioremediation processes being studied on the Ballona Wetlands be affective in different soil types across the world?*Cameron M. Rehmani Seraji 23:55, 16 January 2017 (EST):
- That's not really my area of expertise. My project in the wetlands was sampling soil bacteria and identifying them by their 16S rRNA sequence tags. If phytoremediation is used, i.e., plants are grown to suck up the contaminants and then harvested to discard, it would work as long as the plant could grow there. Dr. Drennan is more of an expert on this than me. — Kam D. Dahlquist 19:56, 18 January 2017 (EST)
- What influenced you to embrace the mathematical side of biology? Was it a specific person? Research you came across? Conor Keith 00:07, 18 January 2017 (EST)
- I started when I was a postdoc and realized that statistics were required to analyze the microarray data that I was working with. I started the modeling project when I came to LMU because I wanted to understand the gene regulatory networks I was studying at a deeper level. So I really got interested in math to use as a tool to answer the biological questions I had. — Kam D. Dahlquist 20:01, 18 January 2017 (EST)
- What prompted you and Dondi to create the XMLPipeDB and what sparked your interest in expanding the amount of open source software available? Margaret J. Oneil 00:22, 19 January 2017 (EST)
- We started XMLPipeDB to solve a problem that GenMAPP was having, i.e., it was difficult to update or create new Gene Databases so that it could be used to analyze those species' data. At the time we started, the computer science professors had an NSF grant to bring open source development into their undergraduate curriculum and I had been frustrated as a postdoc because GenMAPP did not start out as being open source. When Dr. Dionisio explained to me the other facets of open source culture, besides the license, I was in. The rest, as they say, is history. ‐ Kam D. Dahlquist 02:17, 24 January 2017 (EST)
- Prior to starting the modeling project at LMU had you ever been introduced to a similar project during your education that helped shape the current project? *Nika Vafadari 02:34, 19 January 2017 (EST):
- During my postdoc, I had previously worked on analyzing DNA microarray data by visualizing the data on pathways, but it didn't involve modeling, just statistics, and we were not studying gene regulatory pathways, mainly metabolic pathways. My interest in systems biology and gene regulatory networks was inspired, in part, by reading books on my own, especially those by Stuart Kauffman of the Santa Fe Institute (a research institute for complex systems). I attended a talk he gave at UC Santa Cruz, which must have been 20 years ago now. — Kam D. Dahlquist 02:44, 24 January 2017 (EST)
