Zoi-Sci

Google search engine dedicated to “Scientific Jobs/Scientific Positions” only developed by Bioinformatics.fr Team. Job Searchers Click here to try it out.

Okay not a bio utility, but I’m sure this one will be useful. If you are a Del.icio.us user, your bookmarks are unorganized and messy, and it takes time to retrieve the right information, all you need is deliGoo. As the name suggests, it mashes up Del.ici.ous and Google search to create a search engine for your del.ici.ous bookmarks. Works fine with both Firebox (2.0+) and Internet Explorer (6.0+).

It searches sites according to your del.icio.us bookmarks and retrieve useful pages by a word or a phrase it contains as well as creates customized Google search engine using any del.icio.us tag. Found via SoulSoup

I envy bloggers who update their blogs regularly. I almost ignored my poor blog for two months. Though every morning, I make a quiet resolution to myself to blog but end of the day, tiredness and other priorities overcome this. The end result being, as you can see, I’m regularly irregular. Right now trying to catch up…

Stumbled upon this interesting and persuading video of Juan Enriquez ’s presentation at the TED conference from 2004 entitled “Decoding the future with genomics”. Juan talks about the need to utilize the Genomic data generated from the labs around the world and ended the presentation with views about knowledge-based economy determining the fate of nations. Here it goes:

Scientific discoveries, Juan Enriquez notes, demand a shift in code. The shift from cave paintings to hieroglyphics made possible the rise of Egyptian society, the pyramids, and the conquest of other peoples. The shift to binary code brought with it the era of computing and then the Internet, with vast implications for just about every area of human endeavor. Similarly, the rise of genomics has brought a shift in code toward the structure of life, with implications that are slowly revealing themselves. Enriquez argues that our ability to thrive in the culture created by this shift depends on our mastery of it, and companies whose futures lie with the intersecting fates of science, technology, and computing will do well to mind the knowledge gap — and not get swallowed up by it.

Juan is the author of the 2001 best seller “As the Future Catches You” and chairman and CEO of Biotechonomy, a life sciences research and investment firm.

Keynote talk at Bioinformatics Open Source Conference (BOSC) Special Interest Group at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) in Vienna, July 2007 by Carole Goble, University of Manchester

I quite frequently come across blog posts on Medical/ Bioscience 2.0, some of which I have been bookmarking on del.ici.ous or on my personal “To try” folder for later use. With growing number, it has become difficult to track and organize them. I’ve always thought of making a blog post listing all my favorite ones together for my personal reference. Well that seems a daunting task. So, I’m listing some vertical bio search engines to start with.

Though there is a growing number of vertical search engine catering the needs of health science field, but I find that the number is relatively less for biosciences like biotechnology, molecular biology etc., considering the huge community of scientists and students in the field. Most of the old ones are either closed or outdated or simply not impressive enough (Duh! Do I need to provide the link when most of the links are not even working?). I mostly use Google and del.icio.us for my requirements, but I’m on always on a look-out for a decided bio search engine, good enough to make me stick to it for a long time..

Here’s a small collection of few links to vertical search engines in the field of biosciences, which can be used to get more specific hits than broad-based engines like Google.

BioHunt Molecular Biology finder

The database has been automatically created by the Marvin molecular biology sites retrieval robot. Some non relevant documents may sometimes appear.

Kosmix Health

Though this is a health science search section of Kosmix, I found that it gives relevant and well-organized info for bio terms too. To be precise - it instantly creates a homepage for the searched term. Saw this on the “About us” page of the site:

Every organization has a home page on the Web today.
Every user can have a home page on the Web today.
Why not every topic?
At Kosmix, that is what we are all about.
Our focus and passion is simple…
“Build the Unofficial Home Page for Every Topic on the Web”
A starting point for you to explore any topic on the Web

Kosmic review from Mashable:

Kosmix will be powering search for Revolution Health, in order to bring more relevant and up-to-date information regarding treatments, medical conditions and other health-related topics. The goal is to provide better search results than those you’d get from a general web search, and aims to give more targeted content with site-specific resources including articles and clinical trials. This is another example of how online communities can benefit from niche search engines that are more in line with what the end user needs.

BioText

This is a promising project from University of Berkeley (recently published) to develop a flexible, efficient, platform-independent database system infrastructure tailored to the search needs of bioscientists. Their goal is impressive, and I believe that this is what exactly a bioresearcher/ scientist has been wishing for.

• Continuously updated database of articles.
• Systematic integration of synonym matching and normalization.
• Systematic integration with community-accepted lexical ontologies.
• Entity tagging (e.g., protein/gene, receptor, ligand, etc. ).
• Relationship tagging (e.g., treatment-for, binds-to, mutation-of, create-bond, etc).
• “Slicing and dicing’’ subsets of the collection.
• Customization of search setup.
• Flexible, intuitive user interface.

Click here for a detailed description here.

NextBio

Nextbio is the latest one, which I first saw on Scienceroll and appears to be quite useful. This explains it all:

NextBio is a web-based scientific data search engine that offers instant access, search and collaboration across a vast repository of life sciences information. Our query interface makes it easy to ask questions about genes, pathways, study results, disease areas, compound treatments and biomarkers, just to name a few.

It claims to have the largest knowledge base of genomics, proteomics and other specially processed biological, chemical and clinical experimental study results. Another important feature is it also enables researchers and clinicians to import and store their own data to find new insights. You can view a demo here.

Apart from being a life sciences data search engine, it is a community data sharing platform, providing the web 2.0 paradigm of instant access, user-generated content and collaboration to life scientists and clinicians worldwide. It is rapidly gaining popularity with users in over 60 academic institutes and pharmaceutical/ biotechnology companies.

It recently announced its closing of a $7M Series B funding led by Newbury Ventures. The new funds will be used for the further expansion of the search engine. (via)

If you are bored of all these, try searching me and my network on Lijit.

Talking about trust factor as mentioned in bbgm blog, if not me, you can trust my network for relevancy . Well Seriously speaking, I found it cool and will put up the widget on side bar soon.

“Her Own DNA” - Bacterial Drawings by Hunter O’Reilly

These innovative artworks, rightly called “living drawings” by Internationally shown artist and experienced geneticist Hunter O’ Reilly are created using living bioluminescent bacteria grown in seaweed nutrient agar in petri dishes. When photographed in dark, the bacteria illuminates revealing the art. Bacteria contribute to the art as they grow and eventually perish as nutrients are used up, fading away the drawing. The bioluminescent bacterium creates its own light via expression of the lux genes.

The artist takes advantage of the bacteria growing to equal brightness along the entire line drawing. Regions where most of the bacterial growth occurs die the fastest because there are limited nutrient resources in the seaweed nutrient agar. The seaweed nutrient agar holding limited resources serves as an analogy for how we use resources within individuals, families, communities, and the world. As the bacteria die the drawing changes and slowly fades into complete darkness. (via)

Pic Source
More here

Another nifty utility, taping the potential of internet and its search capabilities for biological research, is Addgene - a comprehensive repository of plasmids.

Addgene is a non-profit organization dedicated to providing the scientific community with open, efficient and affordable access to plasmid research tools.

The purpose of Addgene is compiling and distributing plasmids that appear in published articles as well as other useful constructs submitted by scientists. Linking plasmids with publications enables researchers to connect to the data generated from the materials they request.

Plasmids and related articles are searchable by gene name, backbone name, author, or article title or you can also browse through the collection.

Click here to see an example of a plasmid map generated using Addgene’s plasmid mapping program.

If you are a science video freak like me but find searching good quality video on sites like Youtube a time-consuming affair, here’s a search engine called ScienceHack by Rami Nasser, exclusively for science videos.

A pivotal feature of science hack is that every video is reviewed by a scientist, so it claims to fetch you relevant and high quality science videos.

Now in alpha release, you can help it get bigger and better by sending feedback and good science videos or links.

Try searching some videos of topics your interest or just browse through to bump into something new and interesting (like I just did :D).

Found via My Biotech Life

The Sun Center of Excellence for Visual Genomics has been working towards using visual data exploration as a means to shed light on the causes of genetics disease.

Recently they developed 4D visualization virtual real atlas of the human body and other organism, with time being the fourth dimension. The technology behind is the world’s first Java 3DTM-enabled CAVE® (CAVE Automated Virtual Environment - developed at the COE as a visualization tool for Bioinformatics research and development).

4D enables you to virtually view the changes occurring in diseased state or genetically affected individuals and can be used for surgical studies.

The CAVE

Christoph with a part of the human body, picture by Christoph W. Sensen (via)

The fully immersive virtual environment consisting of full projection walls, which is CAVE automated, enables scientists to walk in through the three-dimensional virtual real models of biological systems, including cells, tissues and entire organisms. Read more about CAVE and the technical specifications here.

You can try some of the demos available there like the 4D human heart, Negative 3D reconstruction of vascular canals in human cortical bone from micro-CT scans, Human Skeleton etc..

Hmm…finally completed this long pending post discovered via Microarray Blog.

An article via Bharat Biotech

Can manpower shortage slowdown Indian biotech industry, targeting $5 billion revenue by 2010?
Biotech industry is clearly starved of talent. Over 70% of the two lakh Masters degree holders in the country are jobless and frustrated. With media and industry continuously building hype around the nascent biotech industry, several new courses in the subject have sprung up.

Various universities, All India Council for technical education (AICTE) and University Grants Commission (UGC) are giving approvals to several colleges to start courses in biotechnology. This has built a lot of hype and a huge rush among students to opt for biotechnology courses. However, these colleges do not have proper infrastructure or the wherewithal to groom the students. Many colleges don’t even have the basic physical infrastructure or trained teachers.

To specialise in biotech research, you need advanced skillsets. But most students coming out of colleges today lack practical knowledge and are mere bookworms. It’s like earning a catering technology degree without learning how to cook! To improvise on the practical knowledge and bring in skilled people, every Masters degree programme should start insisting on producing at least two publications to showcase their innovative thoughts. And for that, one needs to have the confidence and willingness to take risks. And if we are able to raise the risk-taking ability and innovation levels, we would be giving industry a booster shot. This has to start right at the college level and needs to be extended to the teaching staff too. It might be a good idea to give biotech college lecturers one month vocational training at Council for Scientific and Industrial Research Labs (CSIR), IIT or Indian Institute of Science (IISc)? Perhaps this practical knowledge will facilitate teaching biotechnology courses in a more refined manner.

Moreover, today’s curricula don’t seem to be anywhere close to matching the industry’s requirements. Limited availability of trained manpower is a big hurdle for the industry that needs certain specific skillsets. Students do make a beeline for project work in leading biotech companies, but their interest is limited to the marks it could fetch them. While one cannot complain of lack of commitment, but for obvious reasons, these students can’t be involved in core R&D. The college managements should step forward and approach the department of biotechnology (DBT) to place these students at CSIR laboratories or give students small project works to hone up their innovative skills. Lest, we may be killing the science of biotechnology.

In the next five years, one can expect a huge shortage of right kind of people. A six to nine months training from DBT or CSIR labs is all that the industry needs rather than absorb an absolute fresher. For the industry to touch $5 billion mark by 2010, we need more people to drive innovation levels in biotech segment and make the country biotech capital of the globe. We need 14,000 doctorate holders from the current strength of 1,400.

-(The writer is chairman, Bharat Biotech International Ltd)