tag:blogger.com,1999:blog-9011593280077944746.comments2021-04-11T00:13:59.378-07:00Quantitative Biology: The Next GenerationLilyhttp://www.blogger.com/profile/09735749642899685953noreply@blogger.comBlogger38125tag:blogger.com,1999:blog-9011593280077944746.post-48766455322762855572021-04-11T00:13:59.378-07:002021-04-11T00:13:59.378-07:00Great article.
متخصص وکالت تهرانGreat article.<br /><a href="http://advocacy.unblog.fr/" rel="nofollow">متخصص وکالت تهران</a><br />alihttps://www.blogger.com/profile/11835830755852577356noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-91301826549719578432014-12-06T13:00:14.159-08:002014-12-06T13:00:14.159-08:00Thank you for this valuable information, I hope, i...Thank you for this valuable information, I hope, it is okay that I bookmarked your website for further references.<br /><a href="http://proofreading-guide.org/" rel="nofollow">proofreading services </a>http://www.sacredhypnogoddess.com/40-days-of-inner-power/https://www.blogger.com/profile/14496654331352618082noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-75085066513356354262014-12-06T12:58:30.580-08:002014-12-06T12:58:30.580-08:00 lol, lol, http://www.sacredhypnogoddess.com/40-days-of-inner-power/https://www.blogger.com/profile/14496654331352618082noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-37976592882446221222014-08-22T20:59:39.955-07:002014-08-22T20:59:39.955-07:00Congrats on the nice paper Lily!Congrats on the nice paper Lily!Anonymoushttps://www.blogger.com/profile/15190169936689078615noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-5687230193418174722014-06-06T09:08:00.612-07:002014-06-06T09:08:00.612-07:00I suppose an oversimplified model is actually an i...I suppose an oversimplified model is actually an inaccurate description of our pathetic thinking. :) Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-49268438736019112962014-05-15T22:25:00.616-07:002014-05-15T22:25:00.616-07:00DORA - check it out:
http://am.ascb.org/dora/
DORA - check it out:<br />http://am.ascb.org/dora/<br />Anonymoushttps://www.blogger.com/profile/15190169936689078615noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-21824283519847984142014-04-23T17:01:32.894-07:002014-04-23T17:01:32.894-07:00That's a good one too.That's a good one too. Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-73208234418510175362014-04-23T14:04:24.734-07:002014-04-23T14:04:24.734-07:00Great comment. My feeling is that those words are ...Great comment. My feeling is that those words are now sufficiently meaningless that we must provide a precise definition when we use them in a particular context.<br /><br />Another one to add to your list is 'regulation'. This word implies understanding but often it hides a lack of understanding.Omerhttps://www.blogger.com/profile/08905832997141370052noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-63480190816618358062014-04-17T11:36:54.678-07:002014-04-17T11:36:54.678-07:00In my opinion, proper term should be “robustness a...In my opinion, proper term should be “robustness analysis”. Modeling papers should include some analysis showing the level of confidence or robustness. Reviewers often ask for parameter sensitivity analysis and it seems fine to include some calculation without telling anything about the model's confidence. For example, doing a local sensitivity analysis is often useless. Bayesian analysis to show parameter distribution is not much useful without a final table or graph showing the confidence interval for the model against certain properties. <br /><br />I believe a model can be useful for narrowing down possibilities, and for justifying or invalidating hypotheses/speculations on data or results. In such cases, parameter sensitivity is not essential. Some models are useful because of their structure and justified thoughts behind their formulations. Anonymoushttps://www.blogger.com/profile/04038460643304753474noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-60372416753356497832014-04-14T08:42:58.481-07:002014-04-14T08:42:58.481-07:00Oh yes, some of these are certainly useful, and it...Oh yes, some of these are certainly useful, and it saves time to use a special word instead of spelling out everything all the time. But yeah - we need to keep in mind that not everyone knows what they mean. Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-66134426282367267012014-04-14T08:39:07.673-07:002014-04-14T08:39:07.673-07:00I appreciate your comment!
:)!I appreciate your comment! <br /><br />:)!Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-46185428563170681372014-04-14T05:13:24.015-07:002014-04-14T05:13:24.015-07:00haha this is awesome :)
I think some of the word ...haha this is awesome :) <br />I think some of the word are very meaningful and useful to the field, but they get used so much that people forget not every audience will understand them (e.g. stochastic, as well as some you mentioned above). A definition or re-phrasing once in a while would be helpful :)Veronicahttps://www.blogger.com/profile/08312742352736579800noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-24512507326920842512014-04-13T17:52:52.248-07:002014-04-13T17:52:52.248-07:00Here are some ideas for q-bingo words: Gillespie, ...Here are some ideas for q-bingo words: Gillespie, design principle, systems biology, synthetic biology. Anonymoushttps://www.blogger.com/profile/15190169936689078615noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-26424061042705578892014-04-05T17:20:54.509-07:002014-04-05T17:20:54.509-07:00Here's a link to a story about Bob Ecke's ...Here's a link to a story about Bob Ecke's interesting research on earthquakes:<br />http://www.lanl.gov/newsroom/publications/1663/2014-april/earthquakes-triggering-earthquakes.phpAnonymoushttps://www.blogger.com/profile/15190169936689078615noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-70107539249487732742014-04-05T17:07:37.146-07:002014-04-05T17:07:37.146-07:00I agree that sensitivity analysis does seem to be ...I agree that sensitivity analysis does seem to be a fetish for some. I also agree that predictions that are good candidates for testing will need to be robust to parameter uncertainties given the usual uncertainties about mechanisms and the typical imprecision of available experimental methods but I don't believe sensitivity analysis, narrowly defined as one of the popular techniques, is an obligatory step in the process of finding such predictions, nor do I believe that sensitivity analysis is the most important way to build confidence in a model. Before a model is used to make an interesting prediction, it should be checked against what's already known about system behavior. I'm wondering if there are any modeling studies of biological systems where sensitivity analysis had a clear and meaningful impact. I can't think of any at the moment. Maybe you know of an example?<br />p.s. In case there's any doubt... :) Ryan, I would love to have you lecture in the q-bio Summer School again. Your lecture is always one of the best.Anonymoushttps://www.blogger.com/profile/15190169936689078615noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-81322377601081400872014-04-05T13:39:48.351-07:002014-04-05T13:39:48.351-07:00Hi Bill,
I think I was that lecturer you mention....Hi Bill,<br /><br />I think I was that lecturer you mention. I don't disagree with you about the value of predictions or about the fact that sensitivity analysis doesn't validate a model. (In fact, I think systems biology has fetishized many forms of "robustness" with little evidence that they are general biological principles.)<br /><br />That said, I do think sensitivity analysis is essential for making "non-obvious testable predictions" that are interesting. Sensitivity analysis will tell you whether your prediction depends on fundamental biological assumptions in the model or whether it depends on (for example) an arbitrary choice to set kcat to 2.0 rather than 13.0. The first case is interesting; the second isn't.Anonymoushttps://www.blogger.com/profile/07675086987980136459noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-26490860686856346182014-03-31T08:59:03.250-07:002014-03-31T08:59:03.250-07:00Thanks! :)
Oh yes, I agree. To move forward from ...Thanks! :)<br /><br />Oh yes, I agree. To move forward from our present understanding, we first need to describe what our present understanding is, and that's definitely part of the reason why we need models. Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-81239198863195086622014-03-30T17:39:49.577-07:002014-03-30T17:39:49.577-07:00Great post, very well written, Lily!
As for the c...Great post, very well written, Lily!<br /><br />As for the comments you guys made, I just wanted to add that we also need models to describe things. True, as our knowledge expands, so do our theories, and old models may be replaced by new models. But until we have a better way to describe a phenomenon, the present model, though it can't be proven right, is still the best way we have to describe said phenomenon. :-)Anonymoushttps://www.blogger.com/profile/09922888671399516573noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-31753710730077570632014-03-30T13:43:38.534-07:002014-03-30T13:43:38.534-07:00That's a good point. A model can be proven wro...That's a good point. A model can be proven wrong, but it can't really be proven right - it can, at most, be supported. Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-28705244100184138092014-03-30T12:48:30.671-07:002014-03-30T12:48:30.671-07:00Great summary.
I would say that models are most u...Great summary.<br /><br />I would say that models are most useful when they can be rejected. Experiments that validate a model prediction do not validate the model since many other models may be able to produce the same prediction. Therefore, I would say that mathematical models can be used to reject hypotheses.Omerhttps://www.blogger.com/profile/08905832997141370052noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-3677174503708456012014-03-29T16:45:26.914-07:002014-03-29T16:45:26.914-07:00The paper mentioned by Veronica is cited >200 t...The paper mentioned by Veronica is cited >200 times according to Google Scholar. Anonymoushttps://www.blogger.com/profile/15190169936689078615noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-77408322405195344892014-03-21T11:15:31.774-07:002014-03-21T11:15:31.774-07:00Interesting: http://en.wikipedia.org/wiki/Extreme_...Interesting: http://en.wikipedia.org/wiki/Extreme_programming_practices<br />I wonder how many of those other practices would help (or not help) the writing process. Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-62315049281049438642014-03-20T22:59:15.677-07:002014-03-20T22:59:15.677-07:00An interesting point of view. I suppose the first ...An interesting point of view. I suppose the first 1/3 is when people are trying the hardest to follow along anyway - in part to decide whether they should make the effort to follow the rest of the talk. Lilyhttps://www.blogger.com/profile/09735749642899685953noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-89047168886906043012014-03-20T20:00:58.174-07:002014-03-20T20:00:58.174-07:00I should add that my old supervisor is one of the ...I should add that my old supervisor is one of the best speakers/lectures I have ever heardRussellhttps://www.blogger.com/profile/06145967804214731309noreply@blogger.comtag:blogger.com,1999:blog-9011593280077944746.post-55866678323622460482014-03-20T19:54:44.597-07:002014-03-20T19:54:44.597-07:00Niels Bohr was also afraid of writing. Apparently ...Niels Bohr was also afraid of writing. Apparently even as a young adult he would dictate to his mother what to write for his work.<br /><br />This sounds like pretty useful advice. My old supervisor once suggested to write a talk in thirds. Make the first third so that everybody can understand. Make the middle third such that 2/3 can understand and then make the last third so that only 1/3 (the specialists) can understand.<br /><br />That way everybody hopefully gets something from itRussellhttps://www.blogger.com/profile/06145967804214731309noreply@blogger.com