Proteopedia

Proteopedia is a collaborative wiki 3D encyclopedia of proteins and other molecules. Proteopedia contains a page for every entry in the Protein Data Bank (>50,000 pages), as well as pages that are more descriptive of protein structures in general, e.g. Proteopedia. This is really useful site for protein structure visualization www.proteopedia.org

Web link reference manager

Free online reference management (web links ..).
Useful one check it out this http://www.connotea.org/ and sign up (similar to mail sign up) and make use of it.

Vadlo - Search engine for research scholar

check it out this search engine http://www.vadlo.com/ . Cartoons are nice check it out the recent one http://www.vadlo.com/Daily_Research_Cartoon.html.

Indian local search engine

check it out this site quite interesting http://www.guruji.com/

Protein crystallography

Hi ,
Check it out this site, if you are interested in protein crystallography http://proteincrystallography.org/

AIGore Nobel Lecture

Read this Nobel Lecture
http://nobelprize.org/nobel_prizes/peace/laureates/2007/gore-lecture_en.html

The softer side of science

Mastering soft skills helps master one's career.

Success in science is about more than mastering lab techniques. It also depends on 'soft' skills such as motivation, personality, research strategy and communication. It is not always easy for well-trained objective truth-seekers to consider soft skills, which are subjective. But they may help you boost your productivity and communicate your science better.

Scientists should shield themselves from discouraging events and develop a 'frustration tolerance' for paper and grant rejections, criticism by well-meaning colleagues and the depressing tedium of data collection. Then there's hypermotivation. To avoid burn-out, try relaxation (sports, yoga, meditation) and a healthy social life. Just as learning requires a quiet consolidation phase to store material in long-term memory, success in science needs intermittent silence.

Personality traits cannot usually be changed, but there are ways to improve one's disposition in the lab. Perfection, for example, can only be expected in pure mathematics or fairy tales. Beware of the 80–20 rule: for perfection, the last 20% of a task may take 80% of the effort — not a wise choice if you want to be productive. Worse, perfectionism is a sure path to leaving projects or papers incomplete.

A related trap is failure to bring a project to publication. A finished experiment may satisfy your curiosity, but data are only of value to your CV and the rest of the world if published. The drive to completion is healthy, if you wish to succeed in science. Many of us have papers that are 90% finished but never submitted. Consider the time you have already invested, how little is left to do and how much effort it would take to get to the same point with another project.

Writer's block can be a major challenge: sitting in front of a blank page, lacking the wherewithal to start writing. This may be linked to the perfectionist trap ("I do not write unless my text is perfect"), but it could also be the result of a lack of ideas, of writing ability or of self-confidence. It is usually the first 10 minutes of writing that are hardest. Try to start writing without worrying about the presentation or structure.

Scientific leadership qualities — exhibiting responsibility, flexibility and trust — are also essential in all aspects of science.

These seemingly simple tasks can be taxing. But improving soft skills is a critical element of science success.

From Nature magazine http://www.nature.com/naturejobs/2008/080529/full/nj7195-694b.html#top

retracted paper from india

I have gone through this paper recently which is retracted from India

RETRACTED: A computational docking study for prediction of binding mode of diospyrin and derivatives: Inhibitors of human and leishmanial DNA topoisomerase-I
Bioorganic & Medicinal Chemistry Letters, Volume 17, Issue 18, 15 September 2007, Page 5281
Sandeep Chhabra, Pooja Sharma, Nanda Ghoshal.

Reason: This is due to use and publication of data by another group that was neither acknowledged nor credited, and was used against the wishes of the co-workers.

Reference : Bioorganic & Medicinal Chemistry Letters

Gromacs-tutorial

Useful tutorial on Gromacs - Molecular Dynamics suite

http://md.chem.rug.nl/education/mdcourse/MDpract.html

Research article with reviewers comment in Biologydirect

I have seen few papers in Biology direct with reviewers comment and authors response. I am surprised to see this. For example, have a look at this article

Various hypotheses on MHC evolution suggested by the concerted evolution of CD94L and MHC class Ia molecules. Biology Direct 2006, 1:3doi:10.1186/1745-6150-1-3

Profiles in science

This is a interesting webpage in NCBI (Many do not know even i). Recently i have read a book on Molecular Modelling, in that book the author has provided this site http://profiles.nlm.nih.gov/

This is the biographies of some scientist. It is interesting. Have a look at it.

How to setup a default application for a file(like word with Microsoft word)

How to setup a default application for a file a particular file type?
text files with gedit or nedit
pdf files with acroread or xpdf
xml files with gedit or nedit

For example

I want all "xml" file types to openwith gedit (text editor).


Right click the file and select "Open with" "other application" you will get window like this (shown below). If you want to choose different editor choose the file types available.


Select the file type you want. I have selected gedit (text editor)


Now i can open all the "xml"(any application) files with gedit text editor

How to submit sequence in genbank (NCBI)

1)

2)


3)

4)



5)


1) Open the NCBI home page (click genbank submission hyperlink)
2) You will get genbank overview(click submit to genbank)
3) You will get submit to genbank (clikc the right side BankIt)
4) You will get BankIt submission form (enter sequence length)
5)You can fill the BankIt sequence submission form

INSTALl-postgresql in linux

This is a quick guide to installing PostgreSQL on a Linux based system. We need to get this up and running before we can write PHP scripts to talk to the database. We need to install PostgreSQL before we can install PHP (since we need the PostgreSQL header files).

This is a little more complicated than installing Apache.

The best bet is to install from packages since this will make things easier, both now and for upgrades.

If you decide to install from source code, you'll need to create a user and compile the source.

Create a PostgreSQL user (you'll need root access). This is who owns the system. I use the "postgres" user and group, you can use something different but it's best to keep it related to the package.

See your system documentation on how to do this (hint - man useradd). Give the user a home directory of /usr/local/pgsql as this is where PostgreSQL defaults to when it installs.

Once all that is done, untar the source:

$ tar -zxf postgresql-.tar.gz (if you got the gzipp'ed version);
or
$ tar -xjf postgresql-.tar.bz2

Jump into the directory:

$ cd postgresql-

(replace with the version you downloaded from the website).

Again, configure has a lot of help:

$ ./configure --help

We'll just install into /usr/local/pgsql and leave the rest as-is:

$ ./configure --prefix=/usr/local/pgsql

Next we have to make it (this will take a while, it takes longer than Apache):

$ make

You will get a line:
All of PostgreSQL successfully made. Ready to install.

when everything is finished.

You'll need to log in as root to do the rest:

$ su -

Go back to the postgresql directory and do:

# make install

PostgreSQL doesn't allow root to start up the server for security reasons, so next you'll have to change the owner of the files:

# chown -R postgres:postgres /usr/local/pgsql

Change to the postgres user:

# su - postgres

Then, change to /usr/local/pgsql:

$ cd /usr/local/pgsql

We need to initialize a database cluster:

$ bin/initdb -D ./data

This will create a /usr/local/pgsql/data directory and initialize it ready for startup and use.

As usual, you can view options by using the --help switch:

$ bin/initdb --help

Then you can start:

$ bin/pg_ctl -D ./data -l data/logfile start

Now that postgresql is started, we need to create a database and another user before we go any further.

You should use a separate database for each of our projects, it's not essential though - it just makes things a little cleaner and easier to understand.

You should also use separate users for each database. This keeps everything separate and 'project a' won't be able to modify any of 'project b's data.

To create a new user in postgresql, it's pretty simple:

$ /usr/local/pgsql/bin/createuser

and follow the prompts - pretty simple :)

The new user should not be able to create new databases or create new users.


To create a database, it's a little different.

$ /usr/local/pgsql/bin/createdb --owner=username databasename

We have to set the owner of the database when we create it, otherwise the 'postgres' user owns it and then we have to grant access to allow our new user to access it.


Now that that's all done, log out of the postgres user, so we're back as root. In the postgres directory, the contrib/start-scripts/ directory has a few system start up scripts

Useful installation instruction from http://www.designmagick.com/article/2/Starting-Out/Installing-PostgreSQL

This is a quick guide to installing PostgreSQL on a Linux based system. We need to get this up and running before we can write PHP scripts to talk to the database. We need to install PostgreSQL before we can install PHP (since we need the PostgreSQL header files).

This is a little more complicated than installing Apache.

The best bet is to install from packages since this will make things easier, both now and for upgrades.

If you decide to install from source code, you'll need to create a user and compile the source.

Create a PostgreSQL user (you'll need root access). This is who owns the system. I use the "postgres" user and group, you can use something different but it's best to keep it related to the package.

See your system documentation on how to do this (hint - man useradd). Give the user a home directory of /usr/local/pgsql as this is where PostgreSQL defaults to when it installs.

Once all that is done, untar the source:

$ tar -zxf postgresql-.tar.gz (if you got the gzipp'ed version);
or
$ tar -xjf postgresql-.tar.bz2

Jump into the directory:

$ cd postgresql-

(replace with the version you downloaded from the website).

Again, configure has a lot of help:

$ ./configure --help

We'll just install into /usr/local/pgsql and leave the rest as-is:

$ ./configure --prefix=/usr/local/pgsql

Next we have to make it (this will take a while, it takes longer than Apache):

$ make

You will get a line:
All of PostgreSQL successfully made. Ready to install.

when everything is finished.

You'll need to log in as root to do the rest:

$ su -

Go back to the postgresql directory and do:

# make install

PostgreSQL doesn't allow root to start up the server for security reasons, so next you'll have to change the owner of the files:

# chown -R postgres:postgres /usr/local/pgsql

Change to the postgres user:

# su - postgres

Then, change to /usr/local/pgsql:

$ cd /usr/local/pgsql

We need to initialize a database cluster:

$ bin/initdb -D ./data

This will create a /usr/local/pgsql/data directory and initialize it ready for startup and use.

As usual, you can view options by using the --help switch:

$ bin/initdb --help

Then you can start:

$ bin/pg_ctl -D ./data -l data/logfile start

Now that postgresql is started, we need to create a database and another user before we go any further.

You should use a separate database for each of our projects, it's not essential though - it just makes things a little cleaner and easier to understand.

You should also use separate users for each database. This keeps everything separate and 'project a' won't be able to modify any of 'project b's data.

To create a new user in postgresql, it's pretty simple:

$ /usr/local/pgsql/bin/createuser

and follow the prompts - pretty simple :)

The new user should not be able to create new databases or create new users.


To create a database, it's a little different.

$ /usr/local/pgsql/bin/createdb --owner=username databasename

We have to set the owner of the database when we create it, otherwise the 'postgres' user owns it and then we have to grant access to allow our new user to access it.


Now that that's all done, log out of the postgres user, so we're back as root. In the postgres directory, the contrib/start-scripts/ directory has a few system start up scripts

Useful installation instruction from http://www.designmagick.com/article/2/Starting-Out/Installing-PostgreSQL

NCBI Resource Locator

What is this thing?

The NCBI Resource Locator provides stable, uniform addressing for NCBI content, making it easy to link to individual records. Some NCBI resources also provide services (like search) through these URLs.
How does it work?

Each URL has the form

http://view.ncbi.nlm.nih.gov///

Where:

* is an NCBI resource (e.g., pubmed, gene, nucleotide, etc.)
* is the action to perform (e.g., search, get, etc.). If is missing, the default verb "get" is used.
* is data used by the action to perform the request

Some examples:

* http://view.ncbi.nlm.nih.gov/pubmed/12345

Show the PubMed record with pmid 12345
* http://view.ncbi.nlm.nih.gov/pubmed/search/cancer

Search PubMed for "cancer"
* http://view.ncbi.nlm.nih.gov/gene/search/human+p53

Search PubMed for "human p53"
* http://view.ncbi.nlm.nih.gov/homologene/search/dystrophin

Search Homologene for "dystrophin"


Reference http://view.ncbi.nlm.nih.gov/

unzip file(bz2,tar) files

use the command "bunzip2 filename.bz2" for unzip the bz2 files
use the command "tar -cvf filename.tar" for unzip the tar files
use the command "tar -xzvf filename.tar.gz for unzip the tar.gz files

How to transfer files using SCP in linux

Use the command to transfer file using SCP in linux

scp filename username@hostname(or ip address):/home/user/ (path)

for eg, in my homology machine i use

scp filename suresh@homology:/home/suresh/

What is the difference between hypothetical protein and putative protein

A hypothetical protein is the one whose function is unknown while a putative is the one in which the function is known but that is determined computationally, it has not been proved experimentally

Bioinformatics.fr

Bioinformatics.fr