Comments on: The promise of bioinformatics http://www.moseshohman.com/blog/2006/03/03/promise-of-bioinformatics/ software development, informatics, etc. Tue, 23 Aug 2011 22:57:24 +0000 hourly 1 http://wordpress.org/?v=3.2.1 By: Moses http://www.moseshohman.com/blog/2006/03/03/promise-of-bioinformatics/comment-page-1/#comment-96 Moses Thu, 06 Apr 2006 16:45:06 +0000 http://www.moseshohman.com/blog/2006/03/03/17#comment-96 <p>Thanks for your comments, Mark. it certainly helps to be able to speak the language of biology if you're writing biological software. There are many kinds of bioinformatics software projects, and in the scenario you describe above, a student writing a bioinformatics thesis, I think it's fair to expect the programmer to have a deeper understanding of the biology. However, for other projects this may not be realistic. You see this all the time in other application domains. For example, at ThoughtWorks our team wrote equipment leasing software. None of the programmers was a leasing expert (or really knew much about leasing at all). This situation was (and is often) mitigated by hiring "business analysts", people who understand the business and have some understanding (sometimes a deep understanding) of software. These people are in a position to notice when programmers don't ask the right questions, can act as proxies for the customer when the customer is not available to answer questions, and in general can translate between programmer-speak and business-speak.</p> <p>Most bioinformatics projects have very small software development teams, so it is perhaps impossible for many of these projects to expect to have someone who could just play a "science analyst" role. However, I think it's perfectly reasonable to try to form a team composed of experts in software who don't understand the biology fully and bioinformaticists with less training in software but a good understanding of the science. This is in fact what my colleague Mike McCormick's group did at the <a href="http://www.fhcrc.org" rel="nofollow">Hutch</a>, and he reports that it works quite well. The nice thing is that the more senior developers teach the bioinformaticists more about writing code, the bioinformaticists teach the developers more about biology, and everyone gets better at what they do in the end.</p> Thanks for your comments, Mark. it certainly helps to be able to speak the language of biology if you’re writing biological software. There are many kinds of bioinformatics software projects, and in the scenario you describe above, a student writing a bioinformatics thesis, I think it’s fair to expect the programmer to have a deeper understanding of the biology. However, for other projects this may not be realistic. You see this all the time in other application domains. For example, at ThoughtWorks our team wrote equipment leasing software. None of the programmers was a leasing expert (or really knew much about leasing at all). This situation was (and is often) mitigated by hiring “business analysts”, people who understand the business and have some understanding (sometimes a deep understanding) of software. These people are in a position to notice when programmers don’t ask the right questions, can act as proxies for the customer when the customer is not available to answer questions, and in general can translate between programmer-speak and business-speak.

Most bioinformatics projects have very small software development teams, so it is perhaps impossible for many of these projects to expect to have someone who could just play a “science analyst” role. However, I think it’s perfectly reasonable to try to form a team composed of experts in software who don’t understand the biology fully and bioinformaticists with less training in software but a good understanding of the science. This is in fact what my colleague Mike McCormick’s group did at the Hutch, and he reports that it works quite well. The nice thing is that the more senior developers teach the bioinformaticists more about writing code, the bioinformaticists teach the developers more about biology, and everyone gets better at what they do in the end.

]]> By: Mark http://www.moseshohman.com/blog/2006/03/03/promise-of-bioinformatics/comment-page-1/#comment-95 Mark Thu, 06 Apr 2006 13:39:01 +0000 http://www.moseshohman.com/blog/2006/03/03/17#comment-95 <p>Lately I've been helping some students in my lab by reviewing their theses and dissertations and giving them feedback. One of the biggest shortcomings of the program is that they don't get enough biology throughout the course of the program, and their theses reflect that. Questions that should have been asked and answered over the course of their projects were never addressed. The biologists that they worked with, often didn't spend enough time on the project with them discussing the relevance and application of their work. This leaves gaping holes in what they could have discovered and places serious limitations on the scientific relevance and value of their work. </p> <p>From an interaction standpoint, it's best to learn as much as you can about the problem space you're dealing with, in order to ask the right questions of your collaborators. That's often difficult to do, if you speak PERL/Python/Java and they speak Molecular Biology/Microbiology/Virology. You have to speak the same language to be on the same page. Even if you're not the one formulating the questions, you have to be able to understand the question and understand its implications.</p> Lately I’ve been helping some students in my lab by reviewing their theses and dissertations and giving them feedback. One of the biggest shortcomings of the program is that they don’t get enough biology throughout the course of the program, and their theses reflect that. Questions that should have been asked and answered over the course of their projects were never addressed. The biologists that they worked with, often didn’t spend enough time on the project with them discussing the relevance and application of their work. This leaves gaping holes in what they could have discovered and places serious limitations on the scientific relevance and value of their work.

From an interaction standpoint, it’s best to learn as much as you can about the problem space you’re dealing with, in order to ask the right questions of your collaborators. That’s often difficult to do, if you speak PERL/Python/Java and they speak Molecular Biology/Microbiology/Virology. You have to speak the same language to be on the same page. Even if you’re not the one formulating the questions, you have to be able to understand the question and understand its implications.

]]> By: Moses http://www.moseshohman.com/blog/2006/03/03/promise-of-bioinformatics/comment-page-1/#comment-83 Moses Sat, 04 Mar 2006 16:27:19 +0000 http://www.moseshohman.com/blog/2006/03/03/17#comment-83 <p>Thanks, Deepak. You make a good point about the historical effects of past failures. I agree that having biologists get some exposure to informatics during their education would help. Ideally this would not just be a few weeks' crash course in Perl or one class on using NCBI's eUtils, but would involve working with actual developers to produce something together, perhaps a cross-discipline lab course between computer science and biology. </p> <p>I also agree that poor communication is a wider problem that exists anywhere people build software for other people. I think the problem is more severe in any field like bioinformatics where the domain is very complex. The onus is on software and (in this case) biologist leaders to make improved communication a priority.</p> Thanks, Deepak. You make a good point about the historical effects of past failures. I agree that having biologists get some exposure to informatics during their education would help. Ideally this would not just be a few weeks’ crash course in Perl or one class on using NCBI’s eUtils, but would involve working with actual developers to produce something together, perhaps a cross-discipline lab course between computer science and biology.

I also agree that poor communication is a wider problem that exists anywhere people build software for other people. I think the problem is more severe in any field like bioinformatics where the domain is very complex. The onus is on software and (in this case) biologist leaders to make improved communication a priority.

]]> By: Deepak http://www.moseshohman.com/blog/2006/03/03/promise-of-bioinformatics/comment-page-1/#comment-82 Deepak Sat, 04 Mar 2006 05:43:23 +0000 http://www.moseshohman.com/blog/2006/03/03/17#comment-82 <p>It is not just bioinformatics that struggles with this, but computation in itself. Even after so many years computer modeling as something different from experiment and somewhat inferior. Part of it stems from days when computational models (this is mostly true for molecular modeling) were so bad, due to the number of approximations required, that a generation of scientists grew up not trusting them. I think that could change. If today's scientist learns how to apply bioinformatics and other computational techniques as part of their college education. IMO that fundamental change, i.e. incorporating informatics and modeling into lab work for all undergraduates, and maybe even in high school will make a big difference.</p> It is not just bioinformatics that struggles with this, but computation in itself. Even after so many years computer modeling as something different from experiment and somewhat inferior. Part of it stems from days when computational models (this is mostly true for molecular modeling) were so bad, due to the number of approximations required, that a generation of scientists grew up not trusting them. I think that could change. If today’s scientist learns how to apply bioinformatics and other computational techniques as part of their college education. IMO that fundamental change, i.e. incorporating informatics and modeling into lab work for all undergraduates, and maybe even in high school will make a big difference.

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