At novoseek, we are determined to making your daily searches for biomedical literature a better, easier and quickier experience. (and this is why we use to write tips, use cases and improve novoseek)

For that reason, we have created a handy my novoseek guide for the members to enjoy the features of my novoseek at its best. If you haven’t signed up yet for a free account on novoseek, feel free to sign up now.

Feel free to download it and see what it has to offer you.

This is the first version so please tell us what other information you would like to read in it.

This is the 3rd and last post of a series of post about the technology behind novoseek. In the first issue we talked about the problem of synonyms, in the second we showed the challenge of dealing with homonyms, in our third issue we would like to share some thoughts behind data organization and its representation which is a common issue to any type of Web application.

I must confess, I am fond of data visualization. I love all those keynotes, or graphics that have great colors, shapes… They catch my attention despite the fact that I might not understand them or that they provide me with irrelevant information. However some of them are really amazing. When I was doing my research on bioinformatics I was desperate looking for ways to represent all the data I had on protein interactions in a way that I could get a big picture at first and then focus on the details. I found a few amazing things at Visual Complexity but not flexible enough. I must confess that I failed in my intention to apply my programming skills to this task.

When I joined Bioalma and I started promoting our first product AKS, I was really excited with one of its main features that represents the relations among concepts based on the co-occurence in the literature. Is a great piece of software that lets you see at-a-glance which concepts are more related and visualize clusters. However, the information behind it was not always understandable.

When we started the novoseek project we decide to embrace the KIS (Keep It Simple) principle. Although we  try to keep up with this philosophy, I must confess that in our meetings the development manager, marketing director and an art director, its hard to say if we are even close to this philosophy.

Regarding the novoseek interface

As you might remember from previous posts, novoseek analyzes all the literature with an algorithm that integrates database information and takes into account the context of terms to annotate them in the literature. So when we started the project and we had all the data from the analysis of all the literature, we asked ourselve “what should we do with it? How could the user take advantage of all this analysis?”. Obviously, putting it in a search engine that is simple, clear and easy to use was our best choice. We needed to start organizing the data and designing a visualization interface to interact with it.

We needed to arrange all that information in a data structure that could give a fast, efficient and scalable service. The scalability issue was a really important concern. We didn’t want to change the data model when the system needed to serve millions of simultaneous petitions.

We also needed to have a picture of what type of information we wanted to display and how the user could interact with it. Based on our experience we knew that we needed to develop something not only simple but also familiar to the end user. We knew that designing an advanced interface with lots of information would be likely to disconcert the users. Our CEO was always telling us “we need to do something that doesn’t need to be explained to use it and understand it”. And so we did.

So the indexing technology and the automatic disambiguation method enabled novoseek to search faster and more efficiently the most relevant documents. We decided to take advantage of that and build what we called Profile. This profile is the result of the analysis that novoseek does taking advantage of the results of our text-mining analysis to build a list of the most relevant concepts to the query. We thought that this list would be really helpful since it gives a quick idea of what are the main themes related to the query. As we thought this list of relevant concepts needed to be interactive, we then added some functionality to it. Whenever you click on one of the terms of the list you get all the documents that take into account the very query term and the clicked concept. You can check examples with our user cases.

After that, we added many other features, some of which are really handy! Others may be a bit more hidden for advanced users that want to make the most out of the system.

However, understanding the users, the way they interact with us, what is useful and what can be removed to keep up with the KIS philosophy is an endless and ongoing process. At Bioalma, we are always studying what would happen if we put this menu here, if we choose this color or if we set up this log-in box there. Indeed, we mix our own craziness with the user suggestions and it is clear that sometimes we come up with a different (or strange) interface. So stay tuned and find out soon the results of our conversation with users and our own schizophrenia.

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.

via fujito

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.

The other day Valentin and I were discussing how scientists confront the time-consuming task of looking for information in the scientific literature. From my experience as a scientist and from conversations with friends and colleagues, we found out that many of them end up in a frustrating situation when searching and that their path to successful searches in Pubmed can be summarized in one of the 4 following options:

1. Direct

We manage to find results from PubMed although in some cases we have to face the use of MeSH terms. Hashtag #nsdirect

2. Ask for help

After some time facing Pubmed search engine without any success, we decide to ask for help from a colleague or a librarian. Some of our friends told us that they don’t they take this path without trying to do it themselves. Hashtag #nsafh

3. Alternatives

After performing some searches in PubMed and not succeeding in our commitment we just look for alternative search engines like Google, 3rd party pubmed tools or obviously novoseek (we asked our friends they what do you expect them to use besides PubMed. Hashtag #nsalt

4. Beer. Why not?

I mean, after a hard working day, what is better than a beer and face the challenge some other day. Hashtag #nsbeer

Take a look at the image below, its so funny and so real

Now we need you to act! What is your path? Tweet this post to your followers adding the #hashtag that better describes you.

1. Direct, this is my path to successful searches in Pubmed
2. Ask for help, this is my path to successful searches in Pubmed
3. Alternatives, this is my path to successful searches in Pubmed
4. Beer, why not?, this is my path to successful searches in Pubmed

Have a great weekend.

We are glad to announce the launch of the biomedical gadgets working thanks to the novoseek’s API. The use of the biomedical gadgets is open to everyone and free. You can get your API Key today and start using the gadgets to extract relevant biomedical information from novoseek and to create biomedical gadgets. In order to create biomedical gadgets, you just have to follow a few steps to publish it on your website or blog.

Gadgets will allow you to publish biomedical information where you want. Gadgets can be published on your blog, website…(where scripts are accepted) and will alllow you to easily extract information from the literature according to your query. With the gadgets you will:

• Enrich your content
• Integrate valuable data
• Display more information
• And no need to know about programming.

There are at this time 2 types of gadgets:

• The Key Concept Gadget allowing you to display the information related to any biomedical concept.
• The Document Gadget allowing you to display the most recent documents related to your search.

Through an intuitive interface, you will create handy gadgets in a few seconds and will be able to publish a gadget where you need it and modifying it as many time as you want. You are also able to create multiple different gadgets.

Let’s have a look at the possibilities brought by the gadgets with a few examples:

• Insert a Document gadget on your Diabetes blog sidebar to keep readers updated on the most recent scientific publications.

Example: 10 latest publications for Diabetes.

• Insert a gadget to show the most relevant disease, pharmacological substances, genes & proteins, chemical substances, organisms, organs & body parts, tissues, biological functions, procedures-techniques, journals, authors -a combination of them or all of them- related to your query.

Example: Tissues, Biological functions and Procedures/techniques related to “chronic granulomatous disease”

• Match the gadget design to your blog’s.

The examples shown previously have a style by default but you can easily change the design colors, width and height during the creation of biomedical gadgets.

Last but not least, we recommend you to watch the tutorial video about the gadgets to see how easy it works.

We’d love to hear from you and know how you are using the gadgets, so feel free to contact us or leave a comment below.