Bio::Blogs#20 - the very late edition

I said I would organize the 20th edition of Bio::Blogs here on the 1st of April but April fools and my current work load did not allow me to get Bio::Blogs up on time.

There were a couple of interesting discussions and blog posts in March worth noting. For example, Neil mentioned a post by Jennifer Rohn started that initiated what could be one of the longest threads in Nature Network :"In which I utterly fail to conceptualize". It started off as small anti-Excel rant but turned in the comments to 1st) a discussion of bioinformatic tools to use, 2nd) a discussion of wet versus dry mindset and how much one should devote to learn the other. Finally it ended up as a exchange about collaborations and how a social networking site like Nature Network could/should help scientists find collaborators. There was even a group started by Bob O'Hara to discuss this last issue further.

I commented on the thread already but can try to expand a bit on it here. Nature Network is positioned as a social networking site for scientists. So far the best that it has to offer has been the blog posts and forum discussions. This is not very different from a "typical" forum. It facilitates the exchange of ideas around scientific topics but NN could try to look at all the typical needs of scientists (lab books, grant managing, lab managing, collaborations, protocols, paper recomendations,etc) and decide on a couple that they could work into the social network site. Ways to search for collaborators and maybe paper recommendation engines that take advantage of your network (network+connotea) are the most obvious and easier to implement. Thinking long term, tools to help manage the lab could be an interesting addition.

Another interesting discussion started from a post by Cameron Neylon on a data model for electronic lab notebooks (part I, II, III). Read also Neil's post, and Gibson's reply to Cameron on FuGE.
How much of the day to day activities and results need to be structured ? How heavy should this structure be to capture enough useful computer readable information ? Although I find these questions and discussion interesting, I would guess that we are far from having this applied to any great extent. If most people are reluctant to try out new applications they will be even less willing to convey their day to day practices via a structured data model. I mentioned recently the experiment under way at FEBS letters journal to create structured abstracts during the publishing process. As part of the announcement the editors commissioned reviews on the topic. It is worth reading the review by Florian Leitner and Alfonso Valencia on computational annotation methods. They argue for the creation of semi-automated tools that take advantage of the automatic methods and the curators (authors or others). The problems and solutions for annotation of scientific papers are shared with digital lab notebooks. It hope that more interest in this problem will lead to easy to use tools that suggest annotations for users under some controlled vocabularies.

Several people blogged about the 15 year old bug found in the BLOSUM matrices and the uncertainty in multiple sequence alignments. See posts by Neil, Kay Lars and Mailund.
Both cases remind us of the importance of using tools critically. The flip side of this is that it is impossible to constantly question every single tool we use since this would slow our work down to a crawl.

In the topic of Open Science, in March the Open Science proposal drafted by Shirley Wu and Cameron Neylon, for the Pacific Symposium on Biocomputing was accepted. It was accepted as a 3 hour workshop consisting of invited talks, demos and discussions. The call for participation is here along with the important deadlines for submissions (talk proposals due June 1st and poster abstracts due the 12th of September).

On a related note Michael Barton has set up a research stream (explained here) He is collecting updates on his work, tagged papers and graphs posted to Flickr into one feed that gives an immediate impression of what he is working on at present time. This is really a great set up. Even for private use withing a lab or across labs for collaboration this would give everyone involved the capacity to tap into the interesting feeds. I would probably not like to have everyone's feeds and maybe a supervisor should have access to some filtered set of feeds or tags to get only the important updates but this looks a step in the right direction. The same way, machines could also have research feeds that I could subscribe too to get updates on some data source.

Also in March, Deepak suggested we need more LEAP (Lightly Engineered Application Products)in science. He suggests that it is better to have one tool that does a job very well than one that does many somewhat well. I guess we have a few examples of this in science. Some of the most cited papers of all time are very well known cases of a tool that does one job well (ex: BLAST).


Finally, some meta-news on Bio::Blogs. I am currently way behind on many work commitments and I don't think I can keep up the (light) editorial work required for Bio::Blogs so I am considering stopping Bio::Blogs altogether. It has been almost two years and it has been fun and hopefully useful. The initial goal of trying to nit together the bioinformatic related blogs and offering some form of highlighting service is still required but I am not sure this is the best way going forward.
Still, if anyone wants to take over from here let me know by email (bioblogs at gmail.com).

call for Bio::Blogs #20

The 20th edition of Bio::Blogs will be posted here by the end of tomorrow. This is very short notice but if anyone would like to contribute please send a few links of the most interesting things of the past month and I will put everything together (email bioblogs at gmail).

Late Links: Bio::Blogs#18 + new blog

I have been away from the web for the last few weeks as I moved to San Francisco to start my first postdoc. I will be working at UCSF in the Lim Lab and the Krogan lab on the evolution of signaling in yeasts. I'll try to blog more about it later during the year. I am looking forward to getting to know the bay area and hopefully make the most of the great (and apparently relaxed) science & technology environment.

Early this month Michael Barton edited another great edition of Bio::Blogs mostly dedicated to open science. He also put together an essay on the subject that is worth reading and commenting on. The next edition of Bio::Blogs will probably come back here to Public Rambling on the 1st of March (unless there is another volunteer).

Also in these last few weeks Lars Juhl Jensen started blogging at Buried Treasure. I met Lars at EMBL while I was doing my PhD and he always had time to help me out when I had some work related question. Like Roland Krause said Lars is one of the most prolific researchers in computational biology I ever met.

Bio::Blogs #17 - call for submissions

The 17th edition of Bio::Blogs will be hosted by Paulo Nuin at Blind.Scientist . Submissions of interesting bioinformatic related blog posts of this month can be sent, until the end of the November, to the usual address (bioblogs at gmail dot com) or to nuin at genedrift dot org.

There is also still time to submit blog posts to the OpenLab 2007 compilation.

Bio::Blogs #16, The one with a Halloween theme

The 16# edition of Bio::Blogs is know available at Freelancing science. Jump over there for summary of what has been going on during this month in the bioinformatic related blogs. If not for anything else then just to have a look at the pumpkin. Thanks again to everyone that participated.
Paulo Nuin from Blind.Scientist has volunteered to host the 17# edition that is scheduled to appear as usual on the 1st of December.

Bio::Blogs #16 - call for submissions

The next edition of Bio::Blogs (bioinformatics blog journal) will be hosted at Freelancing science on the 1st of November. If you find anything this month that you think is interesting to add to this addition send an email to bioblogs at gmail. com until the end of the month. Anyone interested in hosting future edition can also send an email to volunteer.

Bio::Blogs #15 - call for submission

Since there were no volunteers :) I will be hosting the 15th edition of Bio::Blogs here in the blog. I will be gathering some posts from around the web on bioinformatics and other science related topics from the last month and will post about in on the 1st of October. Suggestions are more than welcome. Please email any links to interesting blog posts to bioblogs at gmail dot com.

On a personal note, I have defended my PhD :). This mostly explains the low volume blogging.

Bio::Blogs #14 - Update

The 14th edition of Bio::Blogs will be hosted by Ricardo at My Biotech Life. It will be made available on the 1st of September and submissions can be sent by email as mentioned in his blog post.

Update: The 14th edition is now posted at My Biotech Life. With all the deadlines I had this past month I left it almost until the end to organize a host. Thanks again to everyone that contributed on such short notice.

Is anyone interested in serving as host for the October edition ?

Bio::Blogs#13

A great edition of the monthly Bio::Blogs is up at Neil's blog. This month there are plenty of tutorials and a round up of blog coverage about the ISMB/ECCB 2007 conference.

PDF version for offline reading of the editorial and highlighted posts is here and here (Box.net copy).

If someone wants to give it a try at editing future editions of Bio::Blogs let me know.

Speaking of community projects, the list of webservers published in that last NAR webserver edition are in this Nodalpoint wiki webpage. If you try one of these services spend a minute noting down if it was even available, if it worked well, etc.

Bio::Blogs #13 call for submissions

Neil has kindly agreed to host the next edition of Bio::Blogs, due out on the first of August. Send in links to blog posts of bioinformatics/chemioinformatics/omics/open science related content to bioblogs at gmail and they will be re-directed to him.

BioBlogs #12 and a blogroll update

The 12th edition of Bio::Blogs is out in Nodalpoint. It has been one year of monthly posts (mostly) about bioinformatics. Is anyone interested in hosting the next edition ?

Also, I updated my blogroll to reflect more what I am currently reading. Most updates are in the bioinformatics part but there are a couple of additions in all of them.

Call for Bio::Blogs #12

I am collecting submissions for the 12th edition of Bio::Blogs. Send in links to blog posts you want to share from your blog or that you enjoyed reading in other blogs to bioblogs at gmail until the end of the month. The next edition will be up at Nodalpoint on the 1st of Jully.

Maybe it could be cool to try out a section on papers of the month as voted by everyone (Neil used to do this once in a while). Anyone interested in participating just has to send a link to a paper, published last month and related to bioinformatics, with a short paragraph explaining what is nice about the paper.

Mike over at Bioinformatics Zen is asking how to continue the Tips and Tricks section of Bio::Blogs. He has put up a wiki page on open science in Nodalpoint to collect information for a possible future edition of the special section.

Bio::Blogs# 11

The 11th edition of Bio::Blogs, is online at Nodalpoint. We tried to do something different this time. Michael Barton volunteered to host a special section dedicated to tips and tricks for bioinformatics that is hosted separately in Bioinformatics Zen. Because there were so many posts this month about personalized medicine there is also a special section on that.

There are three separate PDFs for this edition: 1) the main PDF can be found here; 2) The one on personalized medicine can be downloaded here; the one for tips and tricks available from Bioinformatics Zen. Michael did a great job with this special section, with a very cool design.

Bio::Blogs #10

The 10th edition of Bio::Blogs, the bioinformatics blog journal has been posted at Nodalpoint. The PDF can be downloaded from Box.net.

Bio::Blogs #10 - reminder

The May 1st edition of Bio::Blogs will be hosted at Nodalpoint. Anyone can participate by sending in links for interesting blog posts from April (to bioblogs at gmail). If you send in links to your own blog posts please also say if you agree or not to have the post copied to the PDF version for offline reading.

Bio::Blogs #9 - small update

Welcome to the ninth edition of the bioinformatics blog journal Bio::Blogs posted online on the 1st of April of 2007. The archive from previous months can be found at bioblogs.wordpress.com.

Today is an exciting day for bioinformatics and open science in general. I am happy to report on an ongoing project in Nature that has been under wraps for quite a long time. It is called Nature Sherlock and it promises to turn the dream of rich semantic web for scientist a reality. This service is still in closed beta but you can have a look at (http://sherlock.nature.com/) to see that the service does exist and you might from the name get a sense for what it might do. I have been allowed to use Sherlock for some time and according to the FAQ of the main website it has been co-developed by Google and Nature and it is one of the results of meetings that went on during the 1st Science Foo Camp (also co-organized by Google and Nature). Access to the main site requires a beta tester password but I can say that Sherlock looks like a very promising tool. Sherlock is the code-name for the main bot that is set to crawl text and databases from willing providers (current partners include Nature, EBI, NCBI and Pubmed Central) to produce semantic web objects that abide to well established standards in biology. Some of the results, specially regarding the text mining, are of lower accuracy (details can be found on the help pages) but overall it looks like an amazing tool. I hope that they get this out soon.

In this month's Bio::Blogs I have included many posts that were not submitted but I thought were interesting and worth mentioning. This might be a more biased selection but in this way I can make up for the current low number of submission. As in the last edition, the blog posts mentioned were converted into PDF for anyone interested in downloading and reading Bio::Blogs offline (anyway you might enjoy this). There are many interesting comments in online blog posts that I did not include in the PDF, so if you read this offline and find something interesting go online for the discussion.


News and Views
This month saw the announcement of the main findings coming from the Global Ocean Sampling Expedition. Several articles published in PLoS Biology detail the main conclusions of Craig Venter's efforts to sequence the microbial diversity. Both Konrad and Roland Krause blogged some comments on this metagenomics initiative.

Articles
I will start up this section highlighting Stew's post on software availability. Testing around 111 resources taken from the Application Notes published in the March issues of Bioinformatics shows that between 11% to 17% (depending on the year) of these resources are no longer available. Even considering that bioinformatic research runs at very fast pace and that some of these resources might be outdated by now there is no reason why these resources should not be available (as was required for publication).
RPG from Evolgen submitted a post entitled “I Got Your Distribution Right Here” were he analyzes the variation of genome sizes among birds. He concludes by noting that the variability of genome sizes in aves , is smaller than in squamata (lizards and snakes), and testudines (turtles, tortoises, and terrapins). An interesting question might then be why do birds have a smaller distribution of genome sizes. Is there a selection pressure ?
Barry Mahfood submitted a blog post where he ask the question: “Is Death Really Necessary?”. Looking at the human life-expectancy in different periods in time and thinking about what might determine self, Barry thinks that eternal life is achievable in the very near future.

Semantic web/Mach-up/web-services series
This month there were several blog posts regarding mash-ups, web-services and semantic web. All of these relate to the ease of accessing data online and combining data and services together to produce useful and interesting out-comes.
Freebase has a large potential to bring some of the semantic web concept closer to reality. Deepak sent in a link to his description of Freebase and the potential usefulness of the site for scientists. I had the fortune of receiving an invitation to test the service but I did not have time yet to fully explore it.
I hope you saw trough my April fools introduction to Nature Sherlock. Even if Nature Sherlock does not really exist (it is a service to look for similar articles), it is clear that the Nature publishing group is the most active science publisher on the web. Tony Hammond in Nascent gave in a recent blog post a brief description of some of the tools Nature is working on.
While we are waiting for web services and data to become easier to work with we can speed up the process by using web scraping technologies like openKapow (described by me) or dapper (explained by Andrew Perry). These tools can help you create an interface to services that do not provide APIs.

Tips and Tricks
I will end up this months edition with a collection of tips for bioinformatics. Bosco wrote an interesting post - “Notes to a young computational biologist”- were he collects a series of useful tips for anyone working in bioinformatics. There is a long thread of of comments with other people's ideas making it a useful resource. On a similar note Keith Robison, wrote about error messages and the typical traps that might take a long time to debug if we are not familiar with them. (Update) In reply to a recent editorial in PLoS Computational Biology, Chris sent in some tips for collaboration work.
From Neil Saunder's blog comes a tutorial on setting up a reference manager system using LaTeX. I work mostly on a windows machine and I am happy with Word plus Endnote but I will keep this in mind if I try to change to a Linux set up.
Finally I end up this month's edition with a submission from Suresh Kumar on “Designing primer through computational approach”. It is a nice summary of things to keep in mind for primer design along with useful links to tools and websites that might come in handy.

Update - Just to be sure, the Nature Sherlock is as real as the new Google TiSP wifi service.

Bio::Blogs #9 call for submission

The 9th edition of Bio::Blogs will be posted here tomorrow. I will go around the usual blogs and look for interesting blog posts to make a round-up of what happened during the month. I will try to make again an offline version including the blog posts authorized by the authors. Fell free to submit links to bioinformatic related blog posts you find interesting from your blog and any other blogs during today and tomorrow. Submissions can be sent by email to bioblogs at gmail or in a comment to this post.

Bio::Blogs #8

The eighth edition of Bio::Blogs is coming up soon. It is going to be published here on Public Rambling tomorrow night. I almost forgot that this month is shorter than usual :). There are currently 3 submissions sent in. Pick something from your blogs that is bioinformatic related and sent it in (bioblogs at gmail) or leave the link in the comments. Please also let me know if you mind that I create a PDF file including your submission for offline reading. If you don;t have a blog start one and let me know or just send in a link to something that you particularly liked.

Bio::Blogs# 7 and some quick links

The bioinformatics blog journal Bio::Blogs will have it's 7th edition on the 1st of February. We skipped the January edition because of the holidays. It will be hosted by Paras Chopra on BioHacking blog. Anyone can submit the link to their posts on paras1987 {at} gmail or bioblogs {at} gmail until the end of this month.

Some quick links:
Paras released the source code of a Python program for protein structure prediction.

(via Gerstein' blog) Yale university has a podcast. I wish I could convince EMBL's press office to start blogging and/or a podcast.

(via Deepak) The Science Commons blog announced that the three journals published by EMBO and NPG (EMBO reports, EMBO journal and Molecular Systems Biolgoy) will soon start publishing with a creative commons license. More information on the subject can be found in the EMBO site. In the case of Molecular Systems Biology all articles are published in open access but for EMBO Journal and EMBO reports it looks like the author will decide if they wish to pay an extra fee (2000 euros) to publish in open access. Only the articles published in open access will be published with the creative commons license. Adopting the creative commons license will make re-using their papers much easier, hopefully increasing the usefulness of their content.
(disclaimer: I am currently working for Molecular Systems Biology. All opinions expressed in this blog are my own)

Speaking of re-using content. Alf has set up a mirror site for PLoS One. He called it PLoS Too :) and he is using it to try out some ideas on layout, microformats and features like rating. This is one funny thing about the creative commons license. As long as you give credit to the source you are free to re-use the content. Nothing stops a group of people from setting up a new journal, based on those that are published in creative commons, with a different editorial line. For this particular license you can even try to make some money from re-using the content :).