As we know, Bioinformatics is the application of information technology and computer science to the field of molecular biology. Its main purpose is to increase our understanding of biological processes, which is why bioinformatics is constantly evolving and reinventing itself through new discoveries and technology. Some of the major research topics in the field of bioinformatics are sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies and the modeling of evolution. Continuing our efforts to provide our readers with information that might be of much interest in the simplest possible way, as we have previously done with blogposts such as 10 Science PhD Related Blogs or 10+1 Medical Librarian Blogs.

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We thought it would be helpful to share some interesting bioinformatics blogs that can keep you up to date with all kinds of advancements that are being developed in this area and can also help you find information on new software and data mining systems. These are our picks for the Top 15 Bioinformatics Blogs in 2010:

Fisheye Perspective: A Blog about Systems Biology, Bioinformatics, Chemoinformatics, Science and Life in general- by Abhishek Tiwari.



About the author: Abishek Tiwari shares his opinion on issues dealing with bioinformatics. He is a passionate follower of this subject as part of his research interests, studied B.Tech in Bioinformatics in India and is currently getting his PhD in New Zealand.

Description: This blog includes interesting information on other topics such as: chemoinformatics, visual analytics, systems biology, and science as a whole. One of his latest posts, Availability decay of Bioinformatics web resources: Yes widgets can change it, talks about the inaccessibility of bioinformatics software and web resources and how the use of widgets can improve this situation.


Website: http://www.abhishek-tiwari.com


Twitter: @abhishektiwari

What You´re Doing is Rather Desperate: Notes from the life of a bioinformatics researcher



About the Author: Currently located in Australia, Neil Saunders finds a profound joy in science, which he shares through his blog and other publications. The story behind this blog’s name is pretty funny… after Neil gave a speech at work, “come question time, a member of the audience raised her hand and said: It strikes me that what you’re doing is rather desperate. Wouldn’t you be better off doing some experiments?”


Description: We find this blog to be very helpful since Neil spreads his knowledge, research, and new findings to all of his followers. You can find useful information on database-related issues when visiting this blog, where you can also ask questions on topics he is currently or has previously been researching such as biotechnology and biomolecular sciences.


Website: http://nsaunders.wordpress.com/


Twitter: @neilfws

Blind Scientist

About the Author: In Paulo Nuin´s website, www.genedrift.org, you can find information on this bioinformatician´s work, research, sample software tools, and more! Paulo Nuin, Brazilian born bioinformatician finds himself in Canada getting his post-doc.


Description: In this blog, Paulo shares his insight on creating simple Python scripts. He is very well-recognized in the bioinformatics field and Python programming and was asked recently to review a Python Beginner guide from Packt Publishing. If you want to read more about it, take a look at Preview of Python Testing’s beginner Guide.

Website: http://blindscientist.genedrift.org/category/bioinformatics-opinion/


Twitter: @nuin

Yokofakun: A blog about bioinformatics, semantic web, comics and social networks



About the Author: A blog mainly about bioinformatics and the semantic web. Pierre Lindenbaum is a brilliant bioinformatician from France who is very active in social networks. He also includes comics in his blog, which he has constantly been working on since 2005.


Description: Yokofakun is highly recognized throughout the bioinformatics community through social networking tools. You can find a lot of information about software and databases, as well as overviews and tips on their use. A perfect example of his work is found in The Path from EgonWillinghagen to Neo4j, a graph API fro java: my notebook. We encourage you to follow this bioinformatics blog where you can find many interesting codes.


Website: http://plindenbaum.blogspot.com/

Twitter: @yokofakun

DigitalBio: discovering biology in a digital world

About the Author: Dr. Sandra Porter, a bioinformatics teacher in Seattle and President of Digital World Biology, writes about things she is learning and discovering about in this field of study, and gives her opinion on current events that are relevant to the subject matter.


Description: In her article, A ScienceOnline 2010 session mash-up review: Fact checking and trust, she analyzes whether Google sites contain misleading information while searching for biomedical terms. We encourage you to visit her site and share your personal opinion with her community.


Website: http://scienceblogs.com/digitalbio/


Twitter: @digitalbio

Your bones got a little machine (Pansapiens): Ideas are cheap, implementation is expensive; act accordingly.

About the Author: Andrew Perry is an Australian structural biologist and bioinformatician, and this blog´s author.


Description: Mainly dealing with structural bioinformatics and biology, the content found in his blog provides interesting information of current events taking place in these fields. If you are also interested in video games, Andrew writes web applications and games mostly through Python programming. During 2009, his activity took place mainly in Friendfeed and not in the blog itself. Here are the 2009 posts that never made it where you can find information on database services, API´s and much more!


Website: http://blog.pansapiens.com/


Twitter: @pansapiens

Saaen Tist: On bioinformatics and personal productivity



About the Author: A blog on bioinformatics and personal productivity by Flemish bioinformatician, Jan Aerts, who describes himself as “a genetics/genomics researcher who accidentally tumbled down the slope of programming and bioinformatics“.


Description: Focuses on relevant database and software technologies, sharing his experience and opinion after using them. In one of his latest posts you can find information on the 1000 genome project, the kind of input data it includes, and how it would look in a database.


Website: http://saaientist.blogspot.com

Twitter: @jandot

Byte Size Biology: The musings and ravings of a computational biologist about science, computers, music and, you know, stuff

About the Author: With about 5 posts per week, Professor Iddo Friedberg from the Miami University in Ohio, keeps us aware of all kinds of facts dealing with the scientific world using a humoristic approach.


Description: Apart from science, this computational biologist also shares his thoughts on computers, music, and other topics. Iddo also recommends his favorite bioinformatics blogs. One of the blogposts we have enjoyed the most is A Sh*tload of Data , where he talks about understanding the role microbiomes play.


Website: http://bytesizebio.net/

Twitter: @iddux

It´s Not Easy being Genes

About the Author: For all of you Python lovers! Chris Lasher provides information related to genetics, bioinformatics, and computational biology, which are all subjects he studies as a graduate student in Virginia Tech.


Description: Check his blog out for tips on the latest technology in Python.


Website: http://igotgenes.blogspot.com/


Twitter: @gotgenes

Manuel Corpas´Blog: Genomes, Internet, Bioethics and More…



About the Author: Manuel Corpas is a Spanish computational biologist who shares his knowledge through his personal blog where you can find information on many related subjects of interest such as biology, biotechnology, computational bioethics, synthetic biology and more, where we find he is “a lead developer of the DECIPHER database, a “DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources”. We are delighted to see one of our fellow countrymen so active in the bioinformatics landscape!

Description: You can find posts such as 10 Sarcastic Rules on how to be a Bioinformatician, which not only brings humor to what you are reading but gives you useful tips on how to be at your best. It’s a very reliable source of what goes on in this scientific world.


Website: http://manuelcorpas.com

Twitter: @manuelcorpas

Mailund on the Internet: Computer science, bioinformatics, genetics, and everything in between

About the Author: Thomas Mailund, a research associate professor at the Bioinformatics Research Center in Denmark, is very involved in the bioinformatics world and shares his experiences in conferences and workshops, which he attends, as well as other relevant information on hot topics in this field.


Description: This blog can keep you up to date with information that is emerging in these sessions Mailund participates in. One of his latest posts, which we found to be quite interesting, deals with the evolution of health and medicine .


Website: http://www.mailund.dk/ You can also visit his official work homepage for more information.

Blue Collar Bioinformatics

About the Author: Brad Chapman, biologist and programmer, works in the biology department at Massachusetts General Hospital in Boston. His blog offers support to researchers by answering interesting biological questions, using his personal criteria.

Description: In this site you can find blog posts where he shares information about database systems, genes, and other topics that can be helpful for biologists in their daily functions.


Website:http://bcbio.wordpress.com

Friendfeed: http://friendfeed.com/chapmanb

Mass Genomics: Medical genomics in the post-genome era



About the Author: Dan Koboldt is a highly qualified biologist who works in a Genome Sequencing Center in Washington University in St Louis, and keeps us up to date with this subject through his blog, also sharing his many publications on this interesting topic.


Description: This blog focuses on everything dealing with genomics, just like its name suggests Cancer genomics is one of the subjects he focuses on. In one of his most recent posts, Koboldt points out many concepts and issues that were addressed at sessions in Washington University, such as next generation sequencing and molecular techniques.


Website: http://www.massgenomics.org/

Omics! Omics!:A computational biologist’s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery

About the Author: Computational biologist Keith Robinson has worked on genomic and proteomic technologies, currently working in Massachusetts in the cancer drug discovery field.


Description: Through his blog, Robinson shares his findings by using peculiar examples, which will without a doubt leave you yearning for more. Read his latest post on the possibility of sending synchronous messages to actors…quite entertaining!


Website: http://omicsomics.blogspot.com/

Bonus!

Our #15 Top Pick for bioinformatics blogs is Bio Star available at http://biostar.stackexchange.com/ A site for finding information about bioinformatics, computational genomics, and system biology, containing hundreds of questions and answers on these subjects. It’s an extremely helpful tool, which allows you to interact with other individuals that might have your same interests and doubts regarding bioinformatics. We highly recommend it!

After taking a look at this Top 15 Bioinformatics blogs in 2010, we encourage you to try the novoseek’s API, which we think is a great resource to enrich content, integrate data, and display information in your own format. We are eager to see what skilled bioinformaticians will come up with.

Welcome to the MedLib’s Round 1.9. This month, the MedLib’s Round did not specify a special theme. This may have encouraged medical librarians and you to submit articles as 13 16 people took part in this round. It is always interesting to read medical librarians’ concerns as they are using state-of-the-art tools and techniques to work better and face the new challenges of communication, information retrieval and are always keen on sharing their impression on new services and debates. You will notice that this month, the MedLib’s Round leaves room for discussions on Social Media, web 2.0 services and Tips for health.

Thoughts

• David Eddy Delivers Controversial Reinertsen Lecture About Future of Evidence-based Medicine posted at ICSI Health Care Blog by Kent Bottles, MD.

Dr. David Eddy is a controversial doctor that questions the reliability of evidence-based medicine. He was invited at the Institute for Clinical System Improvements by Kent Bottles, Chief Knowledge Officer at this institute in early november. His conference was remarkable for two reasons. First one is that more than 300 people gathered to attend it. Second is that no one would have guessed Dr. David Eddy would challenge people to think about the future of ICSI and of evidence-based medicine. An extensive post you should read to keep updated on the future of evidence based medicine. (Follow Kent Bottles on twitter)

• Technology & Medicine: new screens on Alisha764’s blog

Alisha Miles shares with us her interest for new technologies and their interest for medicine and health information. In that case, she focuses on the new screens available or on the market or to be released soon and wonders about their possible uses. (Follow Alisha764 on twitter)

Social Media in health

• How Can We Help? Roles for Librarians in Public Health on PH/HA News by Alison Aldrich

Alison exposes her feelings after she attended the American Public Health Association conferences. Her post is a nice sum up of the conference and the people that were there as lecturers. The amount of conferences about social media for health matters lets us guess its importance in discussions. She raises a great question about the importance of advocating open access to public health research too. Indeed, she spent a time in the National Library of Medicine’s booth in the exhibit hall where she could talk about one common question: “how can I get all of your journal articles for free?“.

• What is Google Wave and why should I care? on Krafty Library.

Michelle sums up what is google Wave about and how you can use it. This article will be perfect for you to discover, understand and start using Wave in a proper way. She describes how medecial librarians have already created dedicated waves but still doubts about usefulness of the tool. (Follow her on Krafty)

• Manhunt: Google Wave for Community (Emergency?) Communication posted at Eagle Dawg Blog by Nicole S. Dettmar.

Nicole took part in the google wave about the manhunt in Seattle that happened in early december. She shows how powerful was the very google wave as to information exchange and how users helped enriching previous content. At the same time, she raises the problem of false information in waves (new email tool from google encouraging real time exchange) and spam that may get into these new communication channels. (Follow EagleDawg on twitter)

• FDASM Highlights for UM Stakeholders, pt. 1: Early Presenters as SWOT-Plus posted at Emerging Technologies Librarian by Patricia F Anderson

Patricia wrote a great post (the second) on the highlights of the FDASM. The FDASM is an initiative from the FDA about the use of internet and social media for health related communications for FDA-regulated products. This public hearing held in early november was a beginning to knowing and discovering how to use social media channels to communicate about products. In that field, she recalls how the FDA has already been providing essential resources online. There is more to learn and I encourage you to read it. (Follow Patricia F. Anderson on twitter)

Web 2.0 services for health

• Biomedical search on Biomedsearch by Dr. Shock on Shock M.D.

In this article, we learn with Dr Shock about a new tool that wants to provide free access to documents relating to the biomedical field. He explains the functions of this search engine and wonders about whether it can be an alternative to the redesigned pubmed.

• How to switch from one to the other antidepressant by Dr Shock.

There’s one common problem with antidepressant which is either that the antidepressant does not work or provokes side effects. When that happens, you have to switch from one to another. This can be a tricky task and Dr. Shock presents us some great resources websites to manage it. (Follow Dr. Shock on twitter)

• Medpedia Now Includes News & Analysis, Alerts, Q&A by Walter Jessen on HighlightHealth

Walter Jessen focuses here on new functionalities brought recently to Medpedia and create a richer experience for users. Mepdedia is a medical wiki and has useful functionalities. You will now be able to use in Medpedia the following features: News & Analysis from over 150 professionals, Alerts from real time web platforms and Answers (a kind of medical Yahoo Answers). He then wonders about the possibility for Medpedia to become a medical wikipedia thanks to the amount of reliable information it has. (Follow HighlightHealth on twitter)

Tips

• Adding Methodological Filters to MyNCBI posted at Laika’s MedLibLog by Jacqueline

Jacqueline has created a great tutorial to learn how to add methodological filters to MyNCBI. MyNCBI is one’s account on Pubmed. Obviously, creating filters is a must-use option when you are keen on research and need to automate search processes. In that case, she shows how Pubmed allows to create and run advanced filters to save time. It is always nice to read well detailed techniques that will turn the reader in a better prepared person for searches. Jacqueline writes a lot about Pubmed and she has a great experience with it. Enjoy learning with her. (Follow Laikas on twitter)

• How to follow Twitter users in Google Reader on Clinical Cases and Images Blog by Dr. Ves Dimov.

In this post, Dr. Ves Dimov (who has a great blog in medicine) makes us discover a way to easily read Twitter updates without even following the people via Google Reader. Dr. Ves Dimov explains how this approach makes it easier for him to manage multiple information streams. Plus, Google Reader is web-based and can be accessed from any devide with an interent connection. (Follow Dr. Ves Dimov on twitter)

• How to make and maintain a Library Twitter account on DigiCMB by Guus Van Den Brekel

Guus shows in this example of a new twitter account how to fine tune parameters to receive all the possible interesting updates and twitts right into your twitter account. This tutorial will definitely take you to the best practices in terms of interconnection and follow up! (Follow DigiCMB on twitter)

• Allergy Notes: If you think blogs don’t matter, think again: this blog is the number one search result for “allergic rhinitis guidelines” on Allergy News Updated Daily Blog Dr. Ves Dimov.

Interesting reflexion by Dr. Ves Dimov on the role of blogs when looking for information online through search engines. From the example “allergic rhinitis guidelines” which is the first result on Google, and a blog post -hence listed before NEJM- he shares with us his vision of the future of search results. Blogs and fresh content can play a significant role but better quality source should always be sought for. (Follow Dr. Ves Dimov on twitter)

• A review of the main reference management softwares on Knowledge beyond words by Valentin.

Through a detailed post, we describe the main citation managers available out there and their particularity. You should consult this article if you are to decide what is the citation managers most adapted to your needs and uses. There is also the results of a poll launched on twitter asking people what is their favorite citation manager. (Follow novoseek on twitter)

Thank you for reading this MedLib’s Round on Knowledge beyond words. We’d like to help spread Jacqueline’s message who is looking for ideas for a logo and a new name for the MedLib’s Round which is according to Berci, one of the important things of a blog carnival. So feel free to submit her your ideas, it will be much appreciated.

Feel free to subscribe to the RSS feed of MedLib’s Round Blog Carnival. Next MedLib’s Round will be published next January 5th on Dr. Shock’s blog and you can already submit your materials via this form.

Swine Flu epidemics started a couple of weeks ago now and it has been largely covered in social medias. By social medias, I mean all those platforms where one is able to speak and share real-time information about swine flu. Like for other recent and outbreaking news, real-time information has shown its great and useful possibilities. In fact, recently they have been consulted and used to be broadcasted on mainstream channels such as television. I will insist on the “Twitter thing“, but not only and this is why we can talk of social medias.

The importance of Twitter has been largely acknowledged these past months. For example, this man twitting directly about the plane landing in the Hudson river or the Mumbay attacks. These are examples who have settled a new order in information releases. On one because people like you and me would be likely to become reporters -would they want it or not- able to release information and pictures. On the other hand because it would get people involved and react to attacks, threats or needs faster, as it was done for this hospital in Mumbai.

However, Swine Flu is pretty different: the epidemics is best managed by the WHO organization and there is few people like you and me could do besides informing about what is this disease about (H1N1, Influenza, etc). Are social medias information relevant for Swine Flu ? Is everyone entitled to speak about the Swine Flu on real time information platforms and social medias? Are there limits to one’s use of twitter? And, most importantly, are social medias infected with Swine Flu?

I was stuck by the amount of information people have been releasing on Swine Flu, regardless their specialty or their areas of interest. It just seems everybody had something to say and something to share on that matter. I admit that I (as part of the marketing team) decided too to enjoy this phenomenon to put a search example on H1N1 and swine flu in novoseek. But hey, we’re not the black sheep, other search engines did so, I’ll let you guess which ones.

To give you an idea of the phenomenon, let’s check on trends for swine flu in twitter. Obviously it’s been a hot potato on twitter. But not only. And interestingly, searches for this term experimented a great increase…that quickly dropped.

I understand this is something legitimate –getting worried and twitting about it. However not all of the twitts seem to be justified nor important. Indeed, people started joking about it or -even worse- spreading false information. And I sense that the “you can get swine flu by eating pork” comment is about to become a famous example. Trustworthy people have already been writing about it.

Don’t get me wrong, the problem is not in people joking about swine flu but in the information reliability. Since everyone can follow the hot news using the # hashtags in Twitter Search, it triggers a debate. How to find reliable information among users? Who can be trusted? Who should be avoided ? These are questions that matter-of-factly appear to me and should raise your conscience too.

According to the following statistics for Swine Flu in Google Trends we notice that the drop of interest is almost as fast as its rise. Are we dealing with a serious pandemics here, or just some buzz effect? I am wondering…

The fact is swine flu has had its days and information –good or bad- has spread like fire over social medias. People would speak about it on Facebook too. This map shows how people have been updating their status mentioning “swine flu” in it. It has gone west to east.

This is a good illustration of how people started mentioning swine flu in social medias regardless the reliability or truth of information they would state. One more example, people would start making business over it and enjoying the phenomenon, worries or hysteria (no matter how you call it)… It seems like using the Swine Flu keyword was the key to success. You don’t believe me? Have a look at this advertisement in Google when you perform a search for “prevent swine flu“.

You’ll tell me that it’s always been this way, people would tend to enjoy people’s worries and buzz events. But I fear that Swine Flu has reached a new step.

Where are we going with social medias? Is the epidemics matter enough for people to be entitled to tell all sort of things over the internet? Do we have to find a way to select and filter our contacts ? Should we move to other (new?) platforms? There are questions I don’t know how to answer but I’d sure like to have your opinion about.