Non-scientists think research is not a 'real job'

Non-scientists think research is not a 'real job' because scientists don't have deadlines or discrete targets. On the contrary, I say, we are accountable to those who fund us. Investors want financial returns, taxpayers demand medical advances. We are judged by the number and impact factor of our publications. I have friends who have actually calculated the average impact factor of papers published at their institution, hoping to gauge their own competitiveness.

At the Biopolis, we are subject to annual evaluations in which our productivity is rated on a scale of 1 to 5. These determine our bonus and possibly our career prospects. You don't get points for effort: my decision to study a novel protein has proved unwise because I cannot use established reagents and protocols to churn out data and papers. I can ask many questions about a protein of unknown function. But as I was specifically instructed to "focus on publishing my work as it is completed", the key question driving my research must be: what is the minimum amount of data that can coalesce into a paper?

This practical approach is difficult to reconcile with the risk associated with novel or creative projects. It is, however, necessary if I want to stay employed in a world dictated by 'key performance indicators'. We are subject to constant selection pressure. And, to paraphrase Darwin, those who can adapt, survive.

from Nature Jobs section in Nature May 5th issue

Reference manager-tool required for the scientific community

It is great to these many softwares are available for managing references in Nature News. There are around dozen good softwares for reference manager. More for mac/windows. I feel creating one free good reference manager will surely turn the biologist scientist community to your side.

Programs promise to end PDF paper-chase. Researchers are buzzing about a new type of software that allows them to manage their research paper downloads from online journals much more effectively. http://www.nature.com/news/2008/080430//full/453012b.html

Required skills for a computational biologist

I used to visit nature jobs, International Society for Computational Biology (ISCB) and some computational groups . I often see these requirements for a job application in computational biology. It might be useful for the one who wants to become skilled computational biologist.

Python programming language.
Competent in perl programming language
Experience of shell scripting
Working in a Unix / Linux environment.
A good working knowledge of sequence analysis
Experience in functional annotation of biological sequences
SQL/PostgreSQL database design and use
Statistical analysis
Good knowledge of online Bioinformatics resources
HTML, CSS, PHP etc.

An advice to Indian bioinformaticians (so called)

I have visited CMBI site, Netherland. It is surprising to read this information. However, it is absolutely true. I have copied this information from CMBI site . This is one example like this many more

Applying for a position in my group

On average twice per year I hire a PhD student or a post-doc to work with us on one of the two main topics of the group. This stands in a marked contrast to the average of two people per day who ask if I have a job for them. So, what should you do to make more than the 0.5% chance that you have by luck alone?

First of all, I am not different from any other group leader. I only look at applications from people who show immediately in the first three lines of their letter that they have actually spent time preparing the application. Applications from people who only present themselves and just ask for any job are not taken serious. Applications that start with "Dear sir" will not be read. It is YOUR duty as applicant to find out what my group is working on, what kind of people we are looking for, and what you can mean for the group. To do so, look at our WWW page and look at the articles written by the group members over the last three years. If that gives you the impression that you could add something to the group, then you should think how to formulate that concisely and comprehesively without looking very dumb or very arrogant. Make sure the things I must know are on page 1 of the application. Useless information like hobbies, the family name of your mother, the fact that you went to some high-school somewhere, the fact that you have a drivers license, etc., should be skipped, or at best placed on the last page. Make sure that you explain which of your previous experiences you think are relevant for working in our group.

If you work outside 'the west', you have an extra handicap. Not that we simply assume that people from south-america, africa, or south-asia are by definition dumb, but it is very difficult for us to judge what your papers and courses are worth. And flying you in for an interview is too expensive. Coming from outside 'the west' your best bet is a letter of recommendation from a professor with extensive experience in 'the west'. Obviously, a few articles in international journals with you as first author will help very much too. If you write your master-thesis, write it in English and put in somewhere on the WWW so we can see 'how good you are'. There are several other trivial tips. But in general, make sure that we get a good opportunity to judge you, because that is your major bottleneck, being properly evaluated.

Make sure you understand how science is organized in the country where you want to go to. For example, I often get letters from people from India and Pakistan who want to do an internship. As I don't have any idea what that means, I normally answer 'no, sorry'. Obviously, to you it seems stupid that I don't know what an internship is, but my country organized science differently. And as it is you who wants something from me, and not the other way around, you should make sure that I know what you want and what you have to offer.

The points listed above are very general and hold for each job application. If you want to explicitly work with me, you should be a smart scientist, but also a good programmer. We design software to solve biomedical problems. And we will not spend time teaching people how to write software. You should be able to start programming on day 1. I therefore want to see the source code of your last programme of 10000 lines or more. No need to apply when you cannot provide that. (It doesn't need to be scientific software, a game, or a programme to administrate the inventory of the student club is fine too; just as long as it is your software).

Obviously, you can try to write an open application, but that only makes sense if you are a very exceptionally brilliant person, the kind of person so much worth having that we just raise the funds to hire you. Otherwise, look at the list of open position below and see if your job is listed there, and if so apply for the job, using the hints given above.

Good Luck

Gert Vriend

http://www2.cmbi.ru.nl/groups/modeling-and-data-mining/jobs/

STRUCTURE PREDICTION FLOWCHART

STRUCTURE PREDICTION FLOWCHART

Our database

Scripting the Web with PHP

PHP is one of the most popular open source scripting languages for the Web. It’s fast, effective, and very easy to learn. See for yourself. http://www.linux-mag.com/id/820

Creating PDFs in Linux

Nice article in linux magazine

Sharing documents such as papers, reports, and specifications is made easy with Adobe’s Portable Document Format (PDF). Here’s a primer on how to create PDFs on Linux.

http://www.linux-mag.com/id/1983

Chimera - Molecular Modeling software

PRETTY PICTURES PRETTY FAST. Let’s face it, you can stand in front of a lecture hall for an hour, waving your arms, talking about the symmetrical relationships of hemoglobin’s four subunits, or you can display some nicely rendered images and a movie or two and get the same point across in five minutes. Say what you will about today’s students, they respond to multimedia and in some cases have grown to expect it. This is where Chimera shines. Once learned, gorgeous images take just a few minutes to set up and render. In my biochemistry class, I often make structural figures rather than using the textbooks illustrations, or load Chimera in class and walk students through the structure in 3D. This accomplishes two things: 1) I get to highlight what it is I find important in an RNA double helix, an enzyme active site, etc., and 2) it forces me to learn the structural landscape of the molecules rather than relying on the textbook. The rendering styles of Chimera are of course a matter of taste, but frequent readers of the RCSB PDB’s newsletter have already seen what Chimera can do; it is the “go to” program among the staff and is used on many official publications.

So, now that you are convinced to give Chimera a try, how do we make some movies? There are tutorials on the web site, but to start with, you can try this simple set of commands. In your favorite text editor (Notepad in Windows or TextEdit in Mac OS X), create a file called “movie.cmd” and enter the following text:

movie record
roll y 1 360
wait 360
movie stop
movie encode

Save the file, start Chimera and load your molecule of interest. Get it looking how you like, then open the file “movie.cmd” (File… Open…) and watch it go. This script will rotate the molecule about the y axis in 360 steps of 1 degree, then save the movie. When it’s done you should have a file named “chimera_movie.mov” that you can show to your students. If you would like to see some of the movies I use in my Genetics and Biochemistry lectures, or if you would like to use them in your own classes, please visit my website.

---

1. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 25(13): 1605-12.

Reference : Education corner , spring 2008, RCSB Newsletter, Number 37.

Online Bookmark

What is del.icio.us?

del.icio.us is a collection of favorites - yours and everyone else's. You can use del.icio.us to:

• Keep links to your favorite articles, blogs, music, reviews, recipes, and more, and access them from any computer on the web.
• Share favorites with friends, family, coworkers, and the del.icio.us community.
• Discover new things. Everything on del.icio.us is someone's favorite -- they've already done the work of finding it. So del.icio.us is full of bookmarks about technology, entertainment, useful information, and more. Explore and enjoy.

del.icio.us is a social bookmarking website -- the primary use of del.icio.us is to store your bookmarks online, which allows you to access the same bookmarks from any computer and add bookmarks from anywhere, too. On del.icio.us, you can use tags to organize and remember your bookmarks, which is a much more flexible system than folders.

You can also use del.icio.us to see the interesting links that your friends and other people bookmark, and share links with them in return. You can even browse and search del.icio.us to discover the cool and useful bookmarks that everyone else has saved -- which is made easy with tags.

http://del.icio.us/

Biobar tool bar in firefox

Biobar

A power browsing toolbar for the Life Sciences (Biology/Bioinformatics/Medicine). Easily search and retrieve data from over 45 bioinformatics services from the comfort of the toolbar. Links to bioinformatics tools and resources. You can add/replace/change the searched databases and associated terms by following instructions given at http://biobar.mozdev.org/Customize.html.