I think I mentioned this much earlier but let me point to another situation I recently encountered. There are several web sites with epitope prediction servers. The idea is you upload a peptide, select a few parameters, and eventually you get back a list of possible epitopes along with some metrics. So, you may cut/paste a 1-10K sequence and get back hundreds of interesting things and different servers may give different results. What do you expect a typical user to do with this data?
In my case, I had a more complicated task as I was looking for incorrectly translated base sequences that could lead to accidental epitope matches with normal proteins. So, I had to use things like fake ribosomes on some edited chromosome sequences, upload the hypothetical translation product to a series of slicer and dicers ( epitope makers ) and then collate all the results, and then do blast or other searches on these peptides. How do you do that with a web interface at every point? Offhand, what is the use case for a web interface on an epitope server that will routinely return 100's of hits with no uniform way to select interesting and uninteresting results? Unfortunately, I had to write scripts to extract data from the html. In many cases, I could use lynx to render the html so I didn't have to parse html source but you can't always rely on this. As html is meant to be interactive, there is rarely a guarantee from the site that it will be stable. A simple API with a text response option would have addressed my needs using results that the site probably had to generate anyway to make the html results. Now, I don't expect ANSI to issue a standard for epitope information exchange, but there are formats ranging from simple text ( my preference ) to XML ( with lots of canned support) that can be easily parsed and remain stable even as user artwork is changed to accomodate fashion fads. You see this everywhere- from the Securities and Exchange Commission to the US patent office. I hadn't realized that the API idea would need to be "sold" but I guess I under estimated how many people think that the graphics are the model- and I think that I recognize the shortage of skilled people in the computer area and the skill set that many professionals in the area possess so I guess I should have known better :) So, if you are still not convinced and the moderator doesn't get annoyed, it may be worthwile to continue this discussion and see if you have more objections that I can't satisfactorily address because I consider it to be an important problem. > From: [EMAIL PROTECTED] > To: [EMAIL PROTECTED]; [email protected] > CC: [EMAIL PROTECTED] > Subject: RE: [BiO BB] Advanced web query interfaces for biological databases > Date: Tue, 15 Apr 2008 08:16:33 -0400 > > > The punchline, repeated below, is that you still need someway to get > your GUI to talk to your data source. > I guess we are just arguing over publication and stability of the interface. > >> Date: Mon, 14 Apr 2008 21:49:54 -0700 >> From: [EMAIL PROTECTED] > _________________________________________________________________ More immediate than e-mail? Get instant access with Windows Live Messenger. http://www.windowslive.com/messenger/overview.html?ocid=TXT_TAGLM_WL_Refresh_instantaccess_042008 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
