4 February 2008 - Revision history

189.86.107.2: /* Visualizing structures? */

2011-08-12T11:17:02Z

Visualizing structures?

164.51.46.3: /* bionfo-core meeting logistics at ISMB, Toronto. */

2011-08-12T03:08:44Z

bionfo-core meeting logistics at ISMB, Toronto.

Bgrichter: Undo revision 6958 by 67.160.42.255 (Talk)

2009-10-05T16:38:23Z

Undo revision 6958 by 67.160.42.255 (Talk)

Bgrichter: Undo revision 6967 by 68.32.237.90 (Talk)

2009-10-05T16:37:58Z

Undo revision 6967 by 68.32.237.90 (Talk)

68.32.237.90: /* Discussion--How to create students who are much better in bioinformatics skills? */

2009-10-04T12:40:35Z

Discussion--How to create students who are much better in bioinformatics skills?

67.160.42.255: /* Administrative */

2009-09-30T15:50:14Z

Administrative

Bgrichter: Undo revision 6943 by 189.80.21.126 (Talk)

2009-09-04T18:49:06Z

Undo revision 6943 by 189.80.21.126 (Talk)

132.183.4.6: Undo revision 6944 by 124.172.110.149 (Talk)

2009-09-04T18:47:26Z

Undo revision 6944 by 124.172.110.149 (Talk)

124.172.110.149: /* Education For Biologists (Lead by Michael Rebhan): */

2009-08-09T12:23:07Z

Education For Biologists (Lead by Michael Rebhan):

189.80.21.126: /* Administrative */

2009-08-08T15:36:20Z

Administrative

← Older revision		Revision as of 11:17, 12 August 2011
Line 126:		Line 126:
	Dchip [http://biosun1.harvard.edu/complab/dchip/] --some good usage, some not. Can do some simple analysis.		Dchip [http://biosun1.harvard.edu/complab/dchip/] --some good usage, some not. Can do some simple analysis.

−	~~===Visualizing structures?===~~	+	Many many qualtiy points there.
−
−	~~pymol--http://pymol.sourceforge.net/~~
−
−	~~AK--One of the tools of choice for our structural groups. Loads of powerful feature and well as the capability to generate publication quality figures.~~
−
−	~~MAGE and Kinemage: [http://kinemage.biochem.duke.edu/website/kinhome.htm] from Duke. A web based tool to connect structure and display.~~
−
−	~~autodoc [http://autodock.scripps.edu/], is very good for docking calculations~~.

← Older revision		Revision as of 03:08, 12 August 2011
Line 33:		Line 33:


−	~~== bionfo-core meeting logistics at ISMB, Toronto. ==~~	+	If information were scoecr, this would be a goooooal!
−
−
−	Fran—Currently we have 2 BoF sessions scheduled which occur during lunch. There is 1.25 hours allotted for any BoF session. To make best use of the time, some pre-planning of agenda should be accomplished.
−	~~Amongst callers, it was agreed that these times presented the best official ISMB meeting opportunities. Additionally, there would be planned a few dinners for informal gatherings and chat.~~
−	~~Open discussion point: hold a meeting after close of ISMB? There is ½ day left after close. No consensus.~~
−
−	~~'''Time of Conference Call:''' Voting is available to select a time of day to hold this conference call in the future:~~
−	~~[http://www.doodle.ch/geaakssbs6b7c53e.]~~
−	~~Please visit and add your vote for your choice. A day has been chosen on the site but please ignore (it’s required). We are only voting on the time.~~
−	~~Once a time is selected, we can vote on a specific date.~~
−
−	~~===Possible next concall topics (to be held end of April/ beginning in May):===~~
−
−	~~1. Discussion of ePHI within a regulatory and compliance governed research environment. Patient Health Information (PHI) is routinely collected and analyzed together with *omic~~ information (e.g. genotype-phenotype interactions) within informatics groups located within medical schools and academic medical centers. Use of online tools and hosting services are also very accessible and provide utility and collaboration opportunities to the academic researcher. Additionally, institutional review boards and institution’s compliance groups have been frequently seeking guidance from informatics core facilities regarding security and best practice given requests. The discussion could encompass the convergence of these environments and experiences with ensuring privacy of ePHI. Uses of survey monkey to collect patient responses, google docs to share spreadsheets of information have been voiced as possible open-access utilities.
−
−	~~2. large scale analysis and meta-analysis~~, ~~trick, tips and tools. Similar to~~ this ~~concall discussion, we~~ would focus on practices, techniques, obtain feedback from the “school of hard-knocks”, discuss tools, etc. regarding genotyping chip arrays, whole genome studies, combining disparate data sets during meta-analysis, etc.
−
−	3. Update on Next-generation sequencing technologies. Following on initial discussion during the first bioinfo-core concall, the participants could synch on the latest techniques and tools, particulary in mapping, that have emerged within the scientific community.
−
−	~~4. Meetings topic—We were not able to discuss this topic during the call--which seminars and meetings are most effective for bioinformatics core staff and scientists to~~ be ~~introduced to the field and to stay up with new developments.~~
−
−	~~No other topics were brought forth, but there was interest in ePHI (acknowledging it’s scope does not pertain within~~ a ~~basic research environment utilizing model organisms) and Analysis discussions.~~
−

	=Education For Biologists (Lead by Michael Rebhan):=		=Education For Biologists (Lead by Michael Rebhan):=

@@ Line 4: / Line 4: @@
 [[Category:Education]]
-VISvhR  <a href="http://uudmsmtpilop.com/">uudmsmtpilop</a>, [url=http://bhauwcnumfzh.com/]bhauwcnumfzh[/url], [link=http://uvydeeeflssq.com/]uvydeeeflssq[/link], http://datbytcrxesr.com/
+=Administrative=
 =Education For Biologists (Lead by Michael Rebhan):=

@@ Line 33: / Line 33: @@
 UNC group--young people adapt better, amazed by grad student skills.  However, there is the MS office culture where biologists demand an easy GUI with which to interact.
-RC5C8x  <a href="http://lsostcidzkzb.com/">lsostcidzkzb</a>, [url=http://jirhyrpbrnmq.com/]jirhyrpbrnmq[/url], [link=http://axuuxirlttrp.com/]axuuxirlttrp[/link], http://siklmbnkwtkg.com/
+== Discussion--How to create students who are much better in bioinformatics skills? ==
 = Part II: Tools (David Sexton Introduction)=

@@ Line 33: / Line 33: @@
 UNC group--young people adapt better, amazed by grad student skills.  However, there is the MS office culture where biologists demand an easy GUI with which to interact.
-== Discussion--How to create students who are much better in bioinformatics skills? ==
+RC5C8x  <a href="http://lsostcidzkzb.com/">lsostcidzkzb</a>, [url=http://jirhyrpbrnmq.com/]jirhyrpbrnmq[/url], [link=http://axuuxirlttrp.com/]axuuxirlttrp[/link], http://siklmbnkwtkg.com/
 = Part II: Tools (David Sexton Introduction)=

← Older revision		Revision as of 18:47, 4 September 2009
Line 6:		Line 6:
	6T1MKd <a href="http://vejsqxqnrsmm.com/">vejsqxqnrsmm</a>, [url=http://gvugglgjpgou.com/]gvugglgjpgou[/url], [link=http://jlvdwtoergyp.com/]jlvdwtoergyp[/link], http://vlnskpqbedgf.com/		6T1MKd <a href="http://vejsqxqnrsmm.com/">vejsqxqnrsmm</a>, [url=http://gvugglgjpgou.com/]gvugglgjpgou[/url], [link=http://jlvdwtoergyp.com/]jlvdwtoergyp[/link], http://vlnskpqbedgf.com/

		+	=Education For Biologists (Lead by Michael Rebhan):=

		+	After introduction of topic by Michael Rebhan:
		+
		+	AH—worked in 2 companies. Found that there were differences in scientist involvement but mainly due to cultural aspects. In first company the scientists learned the command line, but another company this was not the case. Experience shows that scientists do not try to do anything that doesn't resemble an easy google search. Some even learn to do simple command line usage, especially if it’s a few repetitive commands.
		+
		+	There are training offerings for in-house tools. VectorNTI and another in-house, custom tool is popular. Some scientists have the motivation to learn, but they tend to learn the tools independently.
		+
		+	'''AK post meeting comments:'''
		+	Typically most of our PhD students & postdocs are able to learn anything, (including command-line) if they can see it addressing an immediate need and their training was applied fairly frequently thereafter. Training was of less use where users had infrequent need of the application. Non technical and broad picture idea seminars why and when to search in protein and not DNA space) do have general appeal and work best in a hands-on environment (20min talk - 20min practical) or in a discussion based format.)
		+
		+	Similarly, the UNC core trains scientists on specific tools.
		+
		+	DL—Found that it’s beneficial for biologists to know basic knowledge to analyze data. They are able to do these with relative small help. However, large-scale analysis require core assistance.
		+
		+	AK—overarching factor in training is the biologist’s familiarity with repetitive analysis and then layering on top the laziest ways to that end. Knowledge of the command line fits this paradigm in some cases and there has been acceptance in learning some unix code. Single click answers are very nice for simplicity, but there are those individuals who take on learning tools and techniques themselves.
		+
		+	MR— Biologists are becoming more comfortable with computers overall, but that doesn’t necessarily mean that they would carefully read what is displayed, carefully consider parameters on forms etc. This can be challenging in a training situation for tools that need careful usage to provide meaningful results. We also found that short courses are most popular, and that personalized training related to urgent problems is most effective.
		+
		+	FL—the core at Whitehead at one time provided several formal course offerings: a 1 semester course of lectures, a 2-day intensive course, and a 5 mini course series (lecture and hands on). Topics included sequence analysis, protein analysis, Introduction to UNIX, Perl programming, bioperl, RDBMS’s using MySQL, microarray analysis. However, after a few years, a lot of these offerings were dropped due to attendance and preparation needed. Courses/seminars that are still provided and popular are microarray analysis and introduction to experimentation techniques and statistics for biologist. All materials are freely accessible to the community at [http://jura.wi.mit.edu/bio/education/].
		+
		+	Format has also changed. While once the courses were formal, now providing “Hot Topics” sessions that are specific and targeted 1-hour sessions with online notes posted internally. They have found the scientists interested in learning more are busy and find it hard to commit to a longer session. A recent topic was ”Unix tips and tricks” (how to manipulate large data outside of excel.) . Had 4-5 different labs represented with 12-15 people in attendance.
		+
		+	SJ--short and sweet courses are most valuable. LAMP (Linux Apache ModPerl/Python, etc) courses seem to get a lot of participating bioinformatics people. Also provide courses on specific tools and usually have hundreds sign up. R statistics package, for example, had 40 people turn out on a Saturday. Most people who come are grad students who need to get into the domain. Some are biologists who are not afraid of the technical. However, there is an unmet need amongst the biologists who need help with tools, but they haven't been able to draw them in yet.
		+
		+	UNC group--young people adapt better, amazed by grad student skills. However, there is the MS office culture where biologists demand an easy GUI with which to interact.
		+
		+	== Discussion--How to create students who are much better in bioinformatics skills? ==
		+
		+	MIT has research focused informatics courses in the biology department, but these are not applied.
		+
		+	AH—Germany offers bioinformatics for biologist courses. But even if free, there is not a lot of interest or they are too difficult. Instruction of a more general basis in grad school doesn't make a lot of sense as people are motivated especially when there is direct applicability to their own needs and work.
		+
		+	MR--we can’t expect too much from mainstream biologists, how about people who are in between—those that are very computer savvy and those that need some nurturing.
		+
		+	AK--can't teach everything to everyone. Short vocational training works in many cases.
		+
		+	DS—Vanderbilt is more willing to hire staff than train. The institution perceives this to possess more bang for their buck. They have had good success in creating wikis for document sharing to share knowledge amongst themselves. Experience has shown that a lot of people would rather explore and investigate first on their own without having to ask someone. Given this, it’s easier to look something up on a wiki.
		+	Vanderbilt has a lot of success on using the wiki. If they have a new piece of software, the users usually type up directions and it appears on their wiki.
		+
		+	DL--Education from regular classes teaches theory. researchers need to know details to run certain programs—need to know the practical.
		+
		+	AH—They found that errors that occur usually encourages all questions to the core. It’s better to work together first for training. It’s usually easy to get biologists to understand correct way of doing something but hard to teaching them how to do it right.

	= Part II: Tools (David Sexton Introduction)=		= Part II: Tools (David Sexton Introduction)=

← Older revision		Revision as of 12:23, 9 August 2009
Line 6:		Line 6:
	6T1MKd <a href="http://vejsqxqnrsmm.com/">vejsqxqnrsmm</a>, [url=http://gvugglgjpgou.com/]gvugglgjpgou[/url], [link=http://jlvdwtoergyp.com/]jlvdwtoergyp[/link], http://vlnskpqbedgf.com/		6T1MKd <a href="http://vejsqxqnrsmm.com/">vejsqxqnrsmm</a>, [url=http://gvugglgjpgou.com/]gvugglgjpgou[/url], [link=http://jlvdwtoergyp.com/]jlvdwtoergyp[/link], http://vlnskpqbedgf.com/

−	~~=Education For Biologists (Lead by Michael Rebhan):=~~

−	~~After introduction of topic by Michael Rebhan:~~
−
−	AH—worked in 2 companies. Found that there were differences in scientist involvement but mainly due to cultural aspects. In first company the scientists learned the command line, but another company this was not the case. Experience shows that scientists do not try to do anything that doesn't resemble an easy google search. Some even learn to do simple command line usage, especially if it’s a few repetitive commands.
−
−	There are training offerings for in-house tools. VectorNTI and another in-house, custom tool is popular. Some scientists have the motivation to learn, but they tend to learn the tools independently.
−
−	~~'''AK post meeting comments:'''~~
−	Typically most of our PhD students & postdocs are able to learn anything, (including command-line) if they can see it addressing an immediate need and their training was applied fairly frequently thereafter. Training was of less use where users had infrequent need of the application. Non technical and broad picture idea seminars why and when to search in protein and not DNA space) do have general appeal and work best in a hands-on environment (20min talk - 20min practical) or in a discussion based format.)
−
−	~~Similarly, the UNC core trains scientists on specific tools.~~
−
−	~~DL—Found that it’s beneficial for biologists to know basic knowledge to analyze data. They are able to do these with relative small help. However, large-scale analysis require core assistance.~~
−
−	AK—overarching factor in training is the biologist’s familiarity with repetitive analysis and then layering on top the laziest ways to that end. Knowledge of the command line fits this paradigm in some cases and there has been acceptance in learning some unix code. Single click answers are very nice for simplicity, but there are those individuals who take on learning tools and techniques themselves.
−
−	MR— Biologists are becoming more comfortable with computers overall, but that doesn’t necessarily mean that they would carefully read what is displayed, carefully consider parameters on forms etc. This can be challenging in a training situation for tools that need careful usage to provide meaningful results. We also found that short courses are most popular, and that personalized training related to urgent problems is most effective.
−
−	FL—the core at Whitehead at one time provided several formal course offerings: a 1 semester course of lectures, a 2-day intensive course, and a 5 mini course series (lecture and hands on). Topics included sequence analysis, protein analysis, Introduction to UNIX, Perl programming, bioperl, RDBMS’s using MySQL, microarray analysis. However, after a few years, a lot of these offerings were dropped due to attendance and preparation needed. Courses/seminars that are still provided and popular are microarray analysis and introduction to experimentation techniques and statistics for biologist. All materials are freely accessible to the community at [http://jura.wi.mit.edu/bio/education/].
−
−	Format has also changed. While once the courses were formal, now providing “Hot Topics” sessions that are specific and targeted 1-hour sessions with online notes posted internally. They have found the scientists interested in learning more are busy and find it hard to commit to a longer session. A recent topic was ”Unix tips and tricks” (how to manipulate large data outside of excel.) . Had 4-5 different labs represented with 12-15 people in attendance.
−
−	SJ--short and sweet courses are most valuable. LAMP (Linux Apache ModPerl/Python, etc) courses seem to get a lot of participating bioinformatics people. Also provide courses on specific tools and usually have hundreds sign up. R statistics package, for example, had 40 people turn out on a Saturday. Most people who come are grad students who need to get into the domain. Some are biologists who are not afraid of the technical. However, there is an unmet need amongst the biologists who need help with tools, but they haven't been able to draw them in yet.
−
−	~~UNC group--young people adapt better, amazed by grad student skills. However, there is the MS office culture where biologists demand an easy GUI with which to interact.~~
−
−	~~== Discussion--How to create students who are much better in bioinformatics skills? ==~~
−
−	~~MIT has research focused informatics courses in the biology department, but these are not applied.~~
−
−	AH—Germany offers bioinformatics for biologist courses. But even if free, there is not a lot of interest or they are too difficult. Instruction of a more general basis in grad school doesn't make a lot of sense as people are motivated especially when there is direct applicability to their own needs and work.
−
−	~~MR--we can’t expect too much from mainstream biologists, how about people who are in between—those that are very computer savvy and those that need some nurturing.~~
−
−	~~AK--can't teach everything to everyone. Short vocational training works in many cases.~~
−
−	DS—Vanderbilt is more willing to hire staff than train. The institution perceives this to possess more bang for their buck. They have had good success in creating wikis for document sharing to share knowledge amongst themselves. Experience has shown that a lot of people would rather explore and investigate first on their own without having to ask someone. Given this, it’s easier to look something up on a wiki.
−	~~Vanderbilt has a lot of success on using the wiki. If they have a new piece of software, the users usually type up directions and it appears on their wiki.~~
−
−	~~DL--Education from regular classes teaches theory. researchers need to know details to run certain programs—need to know the practical.~~
−
−	AH—They found that errors that occur usually encourages all questions to the core. It’s better to work together first for training. It’s usually easy to get biologists to understand correct way of doing something but hard to teaching them how to do it right.

	= Part II: Tools (David Sexton Introduction)=		= Part II: Tools (David Sexton Introduction)=