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<title>Giddings lab RSS Feed</title><link>http://bioinfo.med.unc.edu/index.html</link><description>Hot News&#x21;</description><dc:language>en</dc:language><dc:creator>giddings@unc.edu</dc:creator><dc:rights>Copyright 2006-2007 Morgan Giddings</dc:rights><dc:date>2008-01-16T17:03:59-05:00</dc:date><admin:generatorAgent rdf:resource="http://www.realmacsoftware.com/" />
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<lastBuildDate>Wed, 16 Jan 2008 18:09:58 -0500</lastBuildDate><item><title>Two new papers for high accuracy protein ID&#x2c; HMM_Score and PMM </title><dc:creator>giddings@unc.edu</dc:creator><category>Science</category><dc:date>2008-01-16T17:03:59-05:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/HMMScore_release.html#unique-entry-id-10</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/HMMScore_release.html#unique-entry-id-10</guid><content:encoded><![CDATA[We've been working hard lately on a couple of new methods for improving the accuracy of protein identification, and both of these efforts have recently been published in some good journals.


HMM_Score is based on machine learning principles using a hidden Markov model to significantly improve the accuracy of peptide identification for tandem mass spectrometry (MS/MS) data.  

...The Peptide Markov Model (which, it turns out, doesn't really need the "Markov" part to work well) also uses machine learning principles to significantly improve the accuracy of protein identification using peptide mass fingerprinting (PMF).   While many have come to see the PMF approach as out of date due to the advent of ever-better MS/MS based methods, the paper shows that when peptide ion peak intensities are correlated with the peptide sequence, PMF can rival the accuracy of MS/MS based identification.  ]]></content:encoded></item><item><title>Followup: no baby boom?</title><dc:creator>giddings@unc.edu</dc:creator><category>Science</category><dc:date>2007-09-19T17:43:05-04:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/ee833c74f23553f49f34197ee3869f3e-8.html#unique-entry-id-8</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/ee833c74f23553f49f34197ee3869f3e-8.html#unique-entry-id-8</guid><content:encoded><![CDATA[I also agree with the underlying rationale: by the time I reach 65, I may be burnt out on writing grants, and if I don't have to do it anymore, I probably won't.


Since the premise of the original article was related to NIH grant funding, and not teaching, I stand by my original argument: that at or near retirement age, there is a significant withdrawal of involvement by these folks in the grant-getting game, even if it is not officially called "retirement". 

...I can't speak to others who have been making this claim for years on end, but it is undeniable that the baby boomers represent a significant demographic that will reach the "magical" age of 65 soon. 

...Also, as a followup to my theory about feedback loops, not long after I made that post,  I ran into a graduate student who, unprompted, told me he was discouraged by the difficulty of the current funding environment for academic research, and therefore didn't plan to stay in academia after his PhD. ]]></content:encoded></item><item><title>Too many scientists?</title><dc:creator>giddings@unc.edu</dc:creator><category>Science</category><dc:date>2007-09-18T13:34:50-04:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/too-many-scientists.html#unique-entry-id-6</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/too-many-scientists.html#unique-entry-id-6</guid><content:encoded><![CDATA[While it would be foolish to try to make accurate predictions, there are some big trends in demographics that indicate that we are not necessarily in an equilibrium situation, and that the present oversupply of people may change.


...It is my belief that once they retire en masse, filling these positions with qualified replacements will actually be quite challenging, and we may find that the supply/demand ratio has inverted. </li>


...My assertion is from several factors: 1) The increasing investment in top-notch infrastructure and facilities in places like China is beginning to attract qualified researchers to positions elsewhere; and 2) In the aftermath of Sep. 11th, visas have been significantly harder to obtain, and though it has eased somewhat, there is still a perception of difficulty coming to the US.  

...So in sum, I believe that while the problem is worth some thought and attention, in the end there are a number of feedback loops acting, which in combination with demographics, may yield a situation in 10-20 years that may look much the opposite of the situation we are in today (i.e., not enough qualified people for the jobs available).
]]></content:encoded></item><item><title>GFS Version 2</title><dc:creator>giddings@unc.edu</dc:creator><category>Work</category><dc:date>2007-05-23T19:28:50-04:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/87f1b0b231b255d838e7b0b849a0294e-5.html#unique-entry-id-5</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/87f1b0b231b255d838e7b0b849a0294e-5.html#unique-entry-id-5</guid><content:encoded><![CDATA[In other words, if you want to perform a proteomic search against an unannotated genome, or you don't fully trust the computational gene predictions in the database, GFS might be for you.    You can try it at our redesigned website http://gfs.unc.edu, or just drop us a line and we'll send you a link for downloading the full set of source and executables from ProteomeCommons (under a liberal Apache-style license).  

...&bull; MS/MS data - GFS now has two modes to take advantage of tandem MS data, both a "shotgun" mode and a Peptide Mass Fingerprint mode.  


...&bull; A newer cluster/distributed computing implementation, allowing a search to be divvied up into 100's or even 1000's of jobs to take full advantage of available compute resources.
]]></content:encoded></item><item><title>GFS for Windows</title><dc:creator>giddings@unc.edu</dc:creator><category>Work</category><dc:date>2006-06-29T09:39:34-04:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/8af01e57aca559e6a48adc7ca3b3aac2-3.html#unique-entry-id-3</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/8af01e57aca559e6a48adc7ca3b3aac2-3.html#unique-entry-id-3</guid><content:encoded><![CDATA[It seems to run a bit more slowly on Windows than under Linux or OSX on the same processor.    We haven't yet determined the source of this, though we suspect that it has to do with memory allocation speed when using the Gnustep kit under Windows.    However, we've done a lot of overall speed optimization lately, so hopefully it won't be too slow... we welcome user feedback and input, especially if you have insights on this.


...We welcome your feedback about this (remove "remove.these.words." from the email address).
]]></content:encoded></item><item><title>We&#x27;re on the cover of BMC Evolutionary Biology</title><dc:creator>giddings@unc.edu</dc:creator><category>Work</category><dc:date>2006-06-29T09:37:48-04:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/f897d360d84c316f84d86d82ce080f61-0.html#unique-entry-id-0</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/f897d360d84c316f84d86d82ce080f61-0.html#unique-entry-id-0</guid><content:encoded><![CDATA[The front page of the Journal BMC Evolutionary Biology features our paper on the evolution of the Dscam gene family in their  Research Highlights section on the front page.


This is gratifying, since this paper has been a long time coming.    Among other things, the lead author, Mack Crayton, was displaced from his new home in New Orleans while we were in the revision process.  


This paper has now been rated as "highly accessed" by BMC Evolutionary biology.]]></content:encoded></item><item><title>GFS updates</title><dc:creator>giddings@unc.edu</dc:creator><category>Work</category><dc:date>2006-06-02T12:44:57-04:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/708f577c5111377f73bc65b9c5ce9720-2.html#unique-entry-id-2</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/708f577c5111377f73bc65b9c5ce9720-2.html#unique-entry-id-2</guid><content:encoded><![CDATA[For those wondering what's going on with GFS these days, here's a rundown of some highlights (more detail coming in a paper soon);


...We rely on this object kit because it provides extensive functionality such as that which is now present in Java, e.g. lists, arrays, strings, sets, and all sorts of useful stuff.   ...  Next we will work on the Windows port, which is not expected to be difficult, since GnuSTEP is also available for Windows, and the port to GnuSTEP is done.


...However, we are extending the program to operate with MS/MS spectra alone, e.g. for MudPIT type data.  
]]></content:encoded></item><item><title>About the News/Blog page</title><dc:creator>giddings@unc.edu</dc:creator><category>Work</category><dc:date>2006-02-27T12:55:09-05:00</dc:date><link>http://bioinfo.med.unc.edu/Glabblog/files/6dcaade2b13d5056c5469874bb7b3e70-1.html#unique-entry-id-1</link><guid isPermaLink="true">http://bioinfo.med.unc.edu/Glabblog/files/6dcaade2b13d5056c5469874bb7b3e70-1.html#unique-entry-id-1</guid><content:encoded><![CDATA[Our Wiki has been great.    But it is already suffering from major bloat, so we've decided to create a distinct set of pages for outside visitors that are a bit more focused and less diffuse.    Here we'll talk about the latest happenings, and maybe get a little bit philosophical from time to time.    You are still welcome to visit the Wiki if you want to find out more detail about us.
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