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.
Showing posts with label carnivals. Show all posts
Showing posts with label carnivals. Show all posts
Thursday, March 01, 2007
Bio::Blogs #8
Editorial musings
Welcome to the eight edition of the bioinformatics blog journal Bio::Blogs. The archive from previous months can be found at bioblogs.wordpress.com. When this carnival was started, more than eight months ago, it had the primary objective to serve as sort of display for some of the best bioinformatics blog posts on the web and to create incentives for other people to promote their blogs and join in the conversation.
Looking back at the past Bio::Blogs editions I would like to think that we have manage to come with with many interesting posts about bioinformatic conferences, tools and useful computational tips like the DNA analysis series by Sandra Porter (I,II,III,IV,V,VI). Bio::Blogs has also been use to promote tools that have been published in blogs like the Genetic Programming Applet from Pierre and research like the correlation between protein-interaction likelihood and protein age (I and II) that I worked on.
Not everything went as I would hope. The submissions to Bio::Blogs have not picked up as I would expect. Some of this can be explained by poor promotion of my part but it is also due to the small size of the bioinformatics blogging community. In any case I think it is worth maintaining Bio::Blogs up and running for some more time before thinking about stopping this experiment.
In this edition a PDF version of all the posts has been created for anyone interested in downloading, printing and reading some fine posts over coffee or tea. Leave comments or send an email (bioblogs at gmail.com) with your thoughts/ideas for the continuation of this blog journal.I think this printed version also gives a more concrete impression of the potential of blogging for scientific communication.
News and Views
GrrlScientist submitted a report on a recent Science paper describing how moths use their antennae to help them stabilize their flight. Apart from some nasty experiments were they authors removed and glued parts of the antenna the work features some interesting neurophysiology analysis used to characterize the sensitivity of the antennae.
From my blog I picked an entry on network reconstruction. I think the increasing amounts of omics data should be better explored than it currently is and network reconstruction methods are a very good way of achieving this. In this paper, Jason Ernst and colleagues used expression data to reconstruct dynamic transcription regulatory interactions. I will try to continue blogging about the topic in future posts.
Comentaries
PLoS ONE was launched about two months ago and it has produced so far an amazing stream of publications. However the initially proposed goal of generating discussions online to promote post-publication reviews as been lagging. Stew and Alf wrote two commentaries (summited by Greg) regarding the progress of PLoS ONE. They both discuss the current lack of infrastructures to stimulate the online discussions at the PLoS ONE site. Stew goes even further by providing to anyone interested a nice Gresemonkey script to add blog comments to the PLoS ONE papers. I hope Chris Surridge and the rest of the PLoS ONE team start deploying soon some of the tools that they have talked about in their blog. They need to make ONE feel like home, a place were a community of people can discuss their papers.
From Deepak we have a post dedicated to what he dubs EcoInformatics. The importance of using computational methods to analyze ecological changes from the molecules to the ecosystems. The problems range from data access to data management and analysis. The complexity and the different scales of organization (i.e. molecules, environment, ecosystems, disease) make this a very promising field for computational biologists.
From ecological changes we move on to human evolution. Phil tries to introduce the possibility of humanity using technology to improve itself. Having a strong interest myself in synthetic biology and man-machine interfaces I would say that we are still far away from having such control. It is nevertheless useful to discuss the implications of emerging technologies to better prepare for the possible changes.
Reviews and tips
I start this section with a post from a bran-new bioinformatics blog called Bioinformatics Zen. Michael Barton submitted his post on useful tips to get organized as a dry lab scientist. I agree with most of his suggestions. I have try to use slightly fancier methods of organizing my work using project managing tools but I end up returning to a more straightforward folder based approach as well.
Neil Saunders sent in a nice tutorial on building AJAX pages for bioinformatics. It is a very well explained introduction with annotated code. If you were ever interested in learning the basics of AJAX but never invested time in it, here is a good chance to try it.
Editorial musings
Welcome to the eight edition of the bioinformatics blog journal Bio::Blogs. The archive from previous months can be found at bioblogs.wordpress.com. When this carnival was started, more than eight months ago, it had the primary objective to serve as sort of display for some of the best bioinformatics blog posts on the web and to create incentives for other people to promote their blogs and join in the conversation.
Looking back at the past Bio::Blogs editions I would like to think that we have manage to come with with many interesting posts about bioinformatic conferences, tools and useful computational tips like the DNA analysis series by Sandra Porter (I,II,III,IV,V,VI). Bio::Blogs has also been use to promote tools that have been published in blogs like the Genetic Programming Applet from Pierre and research like the correlation between protein-interaction likelihood and protein age (I and II) that I worked on.
Not everything went as I would hope. The submissions to Bio::Blogs have not picked up as I would expect. Some of this can be explained by poor promotion of my part but it is also due to the small size of the bioinformatics blogging community. In any case I think it is worth maintaining Bio::Blogs up and running for some more time before thinking about stopping this experiment.
In this edition a PDF version of all the posts has been created for anyone interested in downloading, printing and reading some fine posts over coffee or tea. Leave comments or send an email (bioblogs at gmail.com) with your thoughts/ideas for the continuation of this blog journal.I think this printed version also gives a more concrete impression of the potential of blogging for scientific communication.
News and Views
GrrlScientist submitted a report on a recent Science paper describing how moths use their antennae to help them stabilize their flight. Apart from some nasty experiments were they authors removed and glued parts of the antenna the work features some interesting neurophysiology analysis used to characterize the sensitivity of the antennae.
From my blog I picked an entry on network reconstruction. I think the increasing amounts of omics data should be better explored than it currently is and network reconstruction methods are a very good way of achieving this. In this paper, Jason Ernst and colleagues used expression data to reconstruct dynamic transcription regulatory interactions. I will try to continue blogging about the topic in future posts.
Comentaries
PLoS ONE was launched about two months ago and it has produced so far an amazing stream of publications. However the initially proposed goal of generating discussions online to promote post-publication reviews as been lagging. Stew and Alf wrote two commentaries (summited by Greg) regarding the progress of PLoS ONE. They both discuss the current lack of infrastructures to stimulate the online discussions at the PLoS ONE site. Stew goes even further by providing to anyone interested a nice Gresemonkey script to add blog comments to the PLoS ONE papers. I hope Chris Surridge and the rest of the PLoS ONE team start deploying soon some of the tools that they have talked about in their blog. They need to make ONE feel like home, a place were a community of people can discuss their papers.
From Deepak we have a post dedicated to what he dubs EcoInformatics. The importance of using computational methods to analyze ecological changes from the molecules to the ecosystems. The problems range from data access to data management and analysis. The complexity and the different scales of organization (i.e. molecules, environment, ecosystems, disease) make this a very promising field for computational biologists.
From ecological changes we move on to human evolution. Phil tries to introduce the possibility of humanity using technology to improve itself. Having a strong interest myself in synthetic biology and man-machine interfaces I would say that we are still far away from having such control. It is nevertheless useful to discuss the implications of emerging technologies to better prepare for the possible changes.
Reviews and tips
I start this section with a post from a bran-new bioinformatics blog called Bioinformatics Zen. Michael Barton submitted his post on useful tips to get organized as a dry lab scientist. I agree with most of his suggestions. I have try to use slightly fancier methods of organizing my work using project managing tools but I end up returning to a more straightforward folder based approach as well.
Neil Saunders sent in a nice tutorial on building AJAX pages for bioinformatics. It is a very well explained introduction with annotated code. If you were ever interested in learning the basics of AJAX but never invested time in it, here is a good chance to try it.
Wednesday, February 28, 2007
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.
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.
Friday, February 02, 2007
Bio::Blogs #7
The February edition of Bio::Blogs was just published in BioHacking. Thanks to Paras for editing it. He highlighted some blogs related to synthetic biology and some of the recent bioinformatics posts from Neil, Sandra and Pierre.
The 8th edition will be coming back here. The participation has been generally going down so Bio::Blogs might, in the near future, morph to something else.
Just to give it a little twist I thought that it could be interesting to add a PDF version of Bio::Blogs (with the permission of the authors of course). So, for the next month entries I will be asking if the authors concede that the blog posts be compiled into a printable document.
Entries can be submitted until the end of February to bioblogs at gmail.
The February edition of Bio::Blogs was just published in BioHacking. Thanks to Paras for editing it. He highlighted some blogs related to synthetic biology and some of the recent bioinformatics posts from Neil, Sandra and Pierre.
The 8th edition will be coming back here. The participation has been generally going down so Bio::Blogs might, in the near future, morph to something else.
Just to give it a little twist I thought that it could be interesting to add a PDF version of Bio::Blogs (with the permission of the authors of course). So, for the next month entries I will be asking if the authors concede that the blog posts be compiled into a printable document.
Entries can be submitted until the end of February to bioblogs at gmail.
Monday, January 29, 2007
Bio::Blogs #7 final call
As Deepak mentioned in his blog, the February edition of Bio::Blogs (the bioinformatics blog journal) is due soon. It will be up on the 2nd of February at BioHacking, so get your blogging pens working. It has been 2 months since the last call. Go have a look at the past two months, pick up one of your posts or a post you liked, related to bioinformatics and send it to the usual bioblogs at gmail.
The 8th edition will be back here on this blog. If anyone is interested in hosting future editions let me know in the comments or by email and I can make a list (including previous editors :).
Let's see how many posts highlighted in Bio::Blogs make it to the next years Science Blogging Anthology ;).
As Deepak mentioned in his blog, the February edition of Bio::Blogs (the bioinformatics blog journal) is due soon. It will be up on the 2nd of February at BioHacking, so get your blogging pens working. It has been 2 months since the last call. Go have a look at the past two months, pick up one of your posts or a post you liked, related to bioinformatics and send it to the usual bioblogs at gmail.
The 8th edition will be back here on this blog. If anyone is interested in hosting future editions let me know in the comments or by email and I can make a list (including previous editors :).
Let's see how many posts highlighted in Bio::Blogs make it to the next years Science Blogging Anthology ;).
Sunday, January 14, 2007
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 :).
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 :).
Saturday, January 06, 2007
Science Blogging Anthology
Coturnix from a Blog Around the Clock is organizing a science blogging anthology. I missed it during the Christmas holidays but the results are due in a couple of days. Here is the list of posts that got nominated and are now being evaluated. One of my posts made the nomination list :) cool.
Last month Roland Krause said that this type of vanity posts (like blog carnivals) are similar to spam blogs. I actually think that there is value in carnivals and other equivalent content promotion activities. They create a cheap reward system that motivates people to produce more and better content. They also provide with a layer of quality rating even if, in the case of carnivals, the posts that are submitted are self contributed. Bloggers tend to submit their best content to the carnivals.
On a related note but with a very different opinion, here is a rant on Web 2.0 And Narcissism (via Rough Type):
Coturnix from a Blog Around the Clock is organizing a science blogging anthology. I missed it during the Christmas holidays but the results are due in a couple of days. Here is the list of posts that got nominated and are now being evaluated. One of my posts made the nomination list :) cool.
Last month Roland Krause said that this type of vanity posts (like blog carnivals) are similar to spam blogs. I actually think that there is value in carnivals and other equivalent content promotion activities. They create a cheap reward system that motivates people to produce more and better content. They also provide with a layer of quality rating even if, in the case of carnivals, the posts that are submitted are self contributed. Bloggers tend to submit their best content to the carnivals.
On a related note but with a very different opinion, here is a rant on Web 2.0 And Narcissism (via Rough Type):
"What he's getting at is that this whole Web 2.0, social networking, virtual community business is essentially a pornography of the self—a projected, fictionalized self that is then worshipped by the slightly less-perfect self."
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