Fro those interested in metagenomics, a meeting will be held July 11-13 at UCSD with many of the major players in the field participating in some way (I am on the planning committee, so no bias here).
This meeting is connected to the new CAMERA Metagenomics Database run out of UCSD (as a Joint Venture with the Venter Institute). I am about to head down to the Scientific Advisory Board meeting for CAMERA. So I am asking anyone out there who is interested in metagenomics to check out CAMERA and let me know what you think. Right now I am I guess kind of an insider/outsider in CAMERA. I am supposed to have a subcontract to Davis to help integrate some phylogenetic tools into the database but alas the Davis office has been a bit lax shall we say about getting my subcontract set up. So until that is set up I guess I am a CAMERA advisor.
Anyway, if anyone has any useful opinions out there about CAMERA I will be happy to share them with those at the SAB meeting.
Tuesday, May 29, 2007
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Just got this press release by email. I am sick of receiving dozens of unsolicited press releases, especially those in topics not related ...
I think CAMERA is a nicely designed database, and the project data are well organized, full of
ReplyDeletemeta-information (localization, depth; etc...) which are very useful (sequence analysis & correlations). But I found CAMERA a bit slow (too much connections? the price of success).
Regarding the metagenomics meeting at UCSD , unfortunately I won't be able to be there (couldn't apply to international student grant travel), will the presentation slides be online? It would be really a nice initiative as for the online access of the presentation slides of the metagenomics meetings held at the Moore Foundation.
Most likely, the entire talks will be put online as videos ... this is what they did for the last meeting.
ReplyDeleteDo you think that CAMERA has really lived up to its goal of integrating metadata with existing tools and through the development of new tools? While it seems like the potential is there, it seems like this final step is largely missing IMO.
ReplyDeleteI am being agnostic about this ... I want to know what other people think about these things. Can you be more specific about what (1) you would like to see and (2) whether you think promised deliverables have or have not been met
ReplyDeleteI am interested in the tools/capabilities that CAMERA uniquely provides. Blast is available at NCBI. It seems CAMERA is uniquely positioned to take advantage of the extensive metadata that have been collected. Yet so far there aren't any tools that facilitate interacting with the metadata to ask ecologically relevant questions.
ReplyDelete1) Right now blast on CAMERA provides a bunch of alignments. I would like to statistics or even a pie chart (something) that indicates what samples are most relevant. For example if I take my gene of interest and blast it against all the reads, I would like to know if its abundance varies with temperature, salinity, or other variables. Is the gene found throughout the ocean or restricted to certain regions.
2) Its not clear exactly what is planned (or for when). All I know is that CAMERA was going to tightly integrate metagenomic metadata.
Regarding "I would like to know if its abundance varies with temperature, salinity, or other variables. Is the gene found throughout the ocean or restricted to certain regions."
ReplyDeleteThat is a great idea, though I am not sure exactly how one would do this. But I will bring this up.
Regarding #2, I think the plans are still a work in progress, but I will suggest they post what their future plans are.
For the occasional user, the CAMERA BLAST is frustratingly slow. Not the BLAST execution, but the weird Google-based interface.
ReplyDeleteFor the non-occasional user: well, there is no real API to run multiple jobs yet. Is something like that in the making?
What does CAMERA offer that is not available at JGI or NCBI? JGI also appear to offer a lot more tools than just a BLAST, and the IMG/M seems to offer what CAMERA aims to be.
ReplyDeleteI think the comparison of IMGM (JGIs system) with CAMERA is worth doing. I think implicitly many of the people on the SAB are doing this. Most people really like the IMGM interface, it seems.
ReplyDeleteBeing involved in CAMERA, I have to admit that several of the comments here are spot on. There was some good talk about what is not working well at CAMERA, I hope that these were pinpointed and solutions were arrived at somewhere off line (at least I didn't a conclusion reached).
ReplyDeleteIts clear that the SAB has many interesting long range ideas about what CAMERA could be and do but until the foundation is solid I don't think any of these issues is relevant today.
I did not get to go to some of the private SAB discussions because as of yesterday I finally got a subcontract to be part of CAMERA. But it looks like there has been some type of consensus about what needs to be done to make it better. I should say, it is clear that a lot of people are using CAMERA and getting some good results. But like with any new system, there are areas that need fine tuning. Again, I am trying to be agnostic and would love for more people out there to try CAMERA and to give feedback.
ReplyDeleteI really like CAMERA the idea of geo-referenced data is really nice, but the first thing that i would like to have in the database is a direct access to blast (right now you have to run a kind of wizard to run blast) or maybe have the two options if you need help of the intuitive wizard.
ReplyDeleteThe other thing I would love to see is maybe not all the blast alignments results, but what about just something like statistics about how abundant is your sequence in different sampling locations, don't know if this is possible but maybe with the data of individual fragment recruitment per location.
And maybe results about fragment recruitment versus all sequenced bacteria up to date.
Finally I really like your blog! nice work :)