Alexis biochemicals › Likes

So does anybody use this? Until the 2008 Briefings in Bioinformatics review article by Zhang et al. http://tinyurl.com/5blwsc I wasn't aware such a thing was out there. This concerns me for two reasons: 1) the original paper for DAS was published in 2001 by Dowell et al. http://tinyurl.com/5jvysp and 2) our lab group's focus is in genome annotation. - Chris Lasher

To echo Chris, I'm a big fan of the rationale and goals behind DAS. but if you check out DASregistry.org, the fact that the vast majority of DAS providers are the same groups that wrote the specs doesn't speak to wide adoption. (Does the length 9k+ word spec http://biodas.org/documen... have something to do with that?) any comments from DAS users/developers? - Andrew Su

I've tried to use the DAS server at UCSC ( http://genome.ucsc.edu/cgi-bin... ) a few years ago. The result was not enough verbose to use the information. - Pierre Lindenbaum

The lofty goals are commendable and something I'm concerned about. I don't believe DAS is the right answer. - Paul J. Davis

It's not hard to imagine a simpler and more flexible mechanism for finding and retrieving annotations from multiple sources (especially for protein sequences). On the other hand it does seem to be working for some people, and what's the alternative if you don't want to spend a lot of effort creating (and advocating) your own spec? - Eric Jain

I actually believe that DAS is absolutely the right solution for some users. In particular, for example, large genome centers and model organism databases seem to use DAS effectively for data sharing. Someone from (or familiar with) those communities care to chime in? (Todd maybe?) Is DAS just not meant for smaller shops and individual users? - Andrew Su

@Andrew if BioDAS is a spec that requires me to hire a full time person to use it, then something is very, very wrong. - Paul J. Davis

Paul, I don't necessarily agree. There are specs that take take a full person to implement/use (thing FDA/FAA/OSHA compliance), and rightly so. The target users of those specs can and should devote a person or team to it. But it's always been unclear to me whether DAS is targeted only at big bioinformatics shops (where it does well), or do they actually intend for the average individual bioinformatician to participate (where I think they don't do so well)... - Andrew Su

Andrew, I can't boil my thoughts down to anything more concise than if a distributed annotation system approaches the complexities of governmental regulation its fundamentally flawed. Its connected to: http://roy.gbiv.com/untangl... - Paul J. Davis

Implementing the spec does look like a lot of work, but presumably you'd use an existing implementation (e.g. Dazzle or LDAS). There it seems all you need to do (once you managed to set up the software) is figure out how to fit your data into GFF. There may be simpler ways to serve such data, but if there is evidence that there are people who are using DAS-enabled clients and would benefit from having access to your data (or you need a buzzword for a grant application), this investment may make sense... - Eric Jain

Paul, touche... but I chose government as something we'd all recognize. Not sure it was the best analogy. Eric, LDAS seems like exactly what would be needed to bring the complex DAS to a longer tail of developers. It hasn't been updated since 2003 though (http://www.biodas.org/downloa...), so I wonder how widely it's actually used... - Andrew Su

I was expecting more DAS defenders/educators here. No? - Andrew Su

I've followed DAS quite closely since 2000. I think there's no doubt the spec is top-heavy, especially DAS 2.0. We are developing a genome wiki (http://genome.biowiki.org/) and DAS 2.0's writeback has been mooted as a possibility. Then again there is some investment in DAS (e.g. by Affymetrix) and I expect that when we reached a certain level of functionality, DAS might well look more appealing. - Ian Holmes

Ian, I'm not sure I understand. The demo at http://genome.biowiki.org/test..., does that use DAS to get genome features? Of all the applications, I would think this would be a best-case scenario for DAS use... - Andrew Su

Correct me if I'm wrong, but nowadays I would say "why don't they use RDF instead of DAS ?" - Pierre Lindenbaum

@Pierre I'm trying to figure that out, myself. There must be a reason; I must keep reading, keep learning. - Chris Lasher

Can someone walk me through how RDF would to the DAS use case? My understanding is that DAS is great for defining genome features. e.g., Exon 4 of Gene X spans from position A to position B on Chromosome Z. How would one express this in RDF? How would you standardize the vocabulary between all the DAS servers providing this type of data? Just starting my RDF education now... - Andrew Su

@Chris: yes, all those tags genome/chromosome/start/end could/should(?) be described as a set of RDF statements... - Pierre Lindenbaum

um, I look at the sequence and count 18–21 bases? - Richard P Grant

Yep, by hand (hell sometimes on paper!) but then I guess I'm old fashioned. I wasn't even allowed to use PCR until the second year of my PhD and then it took us 12 months to get it working (not quite old enough to have been using multiple water baths thought) - Cameron Neylon

NCBI has a new primer tool that uses primer3 and BLAST http://tinyurl.com/5tk67z - Steven

I like Primer3Plus at http://www.bioinformatics.nl/cgi-bin... - Dave Bridges

I find it odd when PhD students come into the office and don't know how to design PCR primers. Don't know what they're teaching them in the lab. I used to design mine all by eye on printouts in my wet days, and it worked just fine. Just point everyone to primer3 now. - Daniel Swan

I used Primer3 and some obscure Mac System 7 applications. Sometimes it is easy as counting the nucleotides, but if PCR was so simplistic as that science would be much easier. - pn

I'm partial to WebPrimer: http://seq.yeastgenome.org/cgi-bin... - it's not just for yeast by a long shot. Rather like Cameron, I didn't get to do a PCR until I was a postdoc. :-) But Steven's link looks good; I used to check that I would amplify something on genomic DNA by using http://genome.ucsc.edu/cgi-bin... - Heather

Paulo, it's 2008. PCR, 90% of the time *is* that simplistic. I teach the students I have lab responsibility for to do it by eye, and to BLAST what they get to check for uniqueness. I started off by doing it on the Mac, years and years ago, but haven't used a primer design program since about 1999. And Cameron, it sounds like we started doing PCR about the same time. Worked first time for me, but took about 3 weeks to make the reagents. - Richard P Grant

Yes, Richard, has been a while that I hadn't been to a lab doing PCR, maybe since 2001 or 2002. But depending on the availability of similar sequences the only way to go is with a program that at least gives you melting temps and some other conditions. - pn

That's why I like ordering from Sigma—you get a melting temp calculation when you enter the sequences. But I only ever use that to match primers, rather than trying to differentiate between different sets. - Richard P Grant

my primer and overall DNA experience is rather restricted to human, mouse and rat mitochondrial genome and the circular mtDNA is a different, inclusive world, I did manual design and primer3 too - Attila Csordas

I've used a couple programs, but unless you're needing primers frequently, Richard's method is probably the best. Check for uniqueness and Tm, then order the two best looking pairs. - Mr. Gunn

'Richard's method is probably the best'—can I put that on my CV? ;) - Richard P Grant

I typically use vi and this primer checking tool at IDT (http://www.idtdna.com/analyze...). And WebCutter or ApE just to check my restriction sites are sensible. - Andrew Perry

@Richard: sure you can, just credit the quote to "some d00d on teh internets" and your credibility is sure to skyrocket. :-) - Bill Hooker

*laugh* - Richard P Grant