Well, Science SPAM never seems to go away. Not sure exactly why it seems to come in waves, but recently I have been getting a lot of email messages from the OMICS publishing group OMICS Publishing Group: An Open Access Publisher
The latest is for the Journal of Bioanalysis & Biomedicine. I love how the message says
“This is not a spam message, and has been sent to you because of your eminence in the field. “
Interestingly, this is the EXACT same wording in messages I used to receive from the horrible Bentham OPEN group. (see one of my complaining posts about this here). I wonder, did Bentham somehow morph into OMICS publishing group? OMICS Publishing group is also trying to promote itself as an Open Access publisher in much the same way Bentham does. I hope for everyone’s sake they are not connected since the last thing we need is more SPAM out there. Anyway, since I have gotten a bunch of emails from various OMICS journals many of which I have no possible scientific connection to, I am giving OMICS my “Science SPAMMER of the month award”.
So , Saturday I got really annoyed with some unsafe street signs in Davis. I wrote some emails to the police and some realtors. I took pictures. I posted a blog post. And so on (see blog here – Davis, CA: Getting more and more annoyed with dangerous Real Estate signs in #DavisCA). Basically, the issues were realtors putting their open house signs in the street and some others putting signs in areas to block the view of oncoming traffic.
And though I got a response from one of the realtors, it was not very convincing. Thus I was more than pleased this AM to get an email back from the Davis Police Department in response to the emails I had sent in to policeweb@cityofdavis.org
And they said two things. First, they had talked to the manager of the apartment complex that had been placing a sign obstructing traffic and the manager was taking it down. And the police were going to send an email to all realtors in the area reminding them that placing their signs in the street or other public right of way was illegal. May seem like a small thing to many, but I have seen a few near crashes due to the realtor signs and worried about crashes due to the apartment sign. And thus to have these issues fixed so quickly made my day.
I must say, I have had nothing but good interactions with the Davis Police when I have sent questions or emails to their non emergency email address.
Just got an announcement regarding this challenge:
Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations | Automated Function Prediction 2011 July 15-16 2011, Vienna, Austria
Here is a description:
CAFA is a community-driven effort. We call upon computational function prediction groups to predict the function of a set of proteins whose true function is sequestered. At the meeting, we will reveal the functions, and discuss the predictions. The CAFA challenge goals are to foster a discussion between annotators, predictors and experimentalists about methodology as quality of functional predictions, as well as the methodology of assessing those predictions. Registration for CAFA starts July 15, 2010 and the CAFA challenge will take place September 15, 2010 through January 15, 2011.See here for more details on how you can enroll in CAFA.
This is near and dear to my heart as I have been working on methods to predict gene function from sequence for some 15 years now. My first paper on this was in 1995 in which I showed that for genes in multigene families, phylogenetic trees of the gene family could help in predicting functions of uncharacterized members of the gene family. More specifically, I suggested that the position of an uncharacterized gene in a gene tree relative to characterized genes could be used to predict its function. I did this for one family in particular – the SNF2 family – but argued that it could be applied to other families. (I think perhaps it was the first time someone had made this specific argument about using trees to predict function, but am not sure)
I then formalized this idea with a few papers (e.g., here and here) describing a “phylogenomic” approach to predicting function (alas, this is when I invented my first omics word). And for many years since, I continued to work on functional prediction methods and continue to do so. When I was at TIGR for eight years I did this both in my own research and helped others with their functional predictions. I firmly believe that evolutionary approached approaches are critical in such functional prediction and have laid this out in a series of talks and papers (e.g., see this more recent one).
Anyway, enough about me. I can argue all I want about how brilliant I am and about how evolutionary methods are the best approach. But arguing is alas not science. What we need are tests and experiments. And that is where things like CAFA come in. In CAFA one can test how well various functional prediction methods work. And the people involved in CAFA (including organizers Iddo Friedberg, Michal Linial, and Predrag Radivojac and others such as Amos Bairoch, Sean Mooney, Patricia Babbitt, Steven Brenner, Christine Orengo and Burkhard RoshRost)) are to be commended for putting this together because we do not have a lot of these activities and need more in all aspects of genomics (and metagenomics too). Others have discussed doing tests of functional prediction methods before, but I am not sure if any have happened per se.
Have a favorite functional prediction method? Enter it in the competition or give a talk on it. And if you are feeling inspired, organize a similar activity in your area of science – testing is a good thing.
See also Iddo Friedberg’s post about this
In addition to the crawdads, the burrowing owls have been out in full force on the Wildhorse Ag buffer trail recently. There are at least 20 if not more living in the tunnels along the trail. Always entertaining.
http://picasaweb.google.com/s/c/bin/slideshow.swf
Here are some pictures from another night of crawdad fishing. We have been going for some walks along the Wildhorse Ag. Buffer trail at night and keep coming upon a few families fishing for crawdads in the creek. This night, they also had one of their cats with them. It was quite entertaining, with the kids lowering McNuggets into the creek and reeling up crawdads in seconds. Then they dumped out the bucket and watched them crawl back to the creek.
http://picasaweb.google.com/s/c/bin/slideshow.swf
I am getting more and more annoyed with the Davis Realtor crowd. They seem to think that they can place signs anywhere they want to promote their sales. Here are some examples I took today, including one sign by Mona DeMasi that forced a couple of kids further into the path of a car while the kids were trying to ride around a circle.
http://picasaweb.google.com/s/c/bin/slideshow.swf
Just a quick one here. Went for a walk last night on the Wildhorse Agricultural Buffer trail near Wildhorse and bumped into a few families “fishing” for crawdads on the bridge over the little creek there. They were catching them just for the kids to look at them and then let them go on the bridge, which entertained my kids quite a bit … here is a slide show of the crawdads:
http://picasaweb.google.com/s/c/bin/slideshow.swf
Well, Here I am for day 2 in Snowbird at a meeting/workshop discussing the potential for “Terrabase metagenomics”. The main point of the meeting is to discuss whether there would be value in massive massive Metagenomic sequencing in one way or another. I note I have enjoyed this meeting so far greatly – nice and small with some really good people.
Yesterday i gave a talk on microbial evolution and a few others talked about other topics (Rob Knight talked about microbiomes, Jeroen Raes discussed multiple Metagenomic projects, and Rachel Mackelprang discussed permafrost metagenomics). I will write more i hope soon about the science side of this meeting. But that is not what I am here to write about today. I am going to tell you what topics were not getting any love so far at this meetings. And this is not a completely snarky thing here – what people complain about does give some feel for what people are thinking about. In no particular order, here are some examples.
Calling on Californians: West Coast Represent! | The Intersection | Discover Magazine
Jonathan Eisen's Lab 