SureshKumar's Bioinformatics Blog

I am Suresh Kumar Sampathrajan. I have completed my PhD degree in bioinformatics from the University of Vienna, Austria in the year 2010. If you want to know more about me and my research,please click the menus at the top.

I have started this bioinformatics blog mainly for undegraduate and postgraduate students of bioinformatics. This blog will serve as an open resource material for the students and for those who wish to know about bionformatics. This blog contains video tutorials, tips, bioinformatics software downloads, articles on bioinformatics and career opportunities.

Introduction to Internet -Video lecture Series -Watch Online for free

Introduction to Internet -Video lecture Series -Watch Online for free

Overview of Biochemistry -Video lecture Series -Watch Online for free

Overview of Biochemistry -Video lecture Series -Watch Online for free

Metabolism -Video lecture Series -Watch Online for free

Metabolism -Video lecture Series -Watch Online for free





Bioenergetics -Video lecture Series -Watch Online for free

Bioenergetics -Video lecture Series -Watch Online for free



Nucleic Acids -Video lecture Series -Watch Online for free

Nucleic Acids -Video lecture Series -Watch Online for free





Vitamins and Coenzymes -Video lecture Series -Watch Online

Vitamins and Coenzymes -Video lecture Series -Watch Online for free



Carbohydrates -Video lecture Series -Watch Online for free

Carbohydrates -Video lecture Series -Watch Online for free



Membrane Transport -Video lecture Series -Watch Online for free

Membrane Transport -Video lecture Series -Watch Online for free

Lipids and Membranes -Video lecture Series -Watch Online

Lipids and Membranes -Video lecture Series -Watch Online for free



Myoglobin and Hemoglobin -Video lecture Series -Watch Online for free

Myoglobin and Hemoglobin -Video lecture Series -Watch Online for free

Enzyme Mechanisms-Video Lecture Series-Watch Online

Enzyme Mechanisms-Video Lecture Series-Watch Online for Free



Introduction to Enzymes-Video Lecture Series-Watch Online





Protein Structure-Lecture Series-Video-Watch Online

Protein Structure-Lecture Series-Video-Watch Online for Free









Contents
Aminoacid structures and properties, Hydrophobicity-hydropathy plots, Protein hierarchy, Secondary structure elements, Alpha helices and beta sheets, construction of helical wheel, properties & prediction of protein structure, classes of proteins based on structure & solubility, forces driving protein folding, Thermodynamics of protein folding etc

Basic Unix/Linux Commands-Video tutorial-Watch Online




Learn the basic Unix/Linux commands.

This video gives an overview of the basic commands

ls, ls -F, pwd
cd, cd .., cd (nothing)
mkdir, rmdir
rm, rm -r
cp, mv, date
cat, more
#, whoami
who, who am i, w
man, clear, *arguments

Not mentioned: hidden files
Every file that start with a dot (.) is considered a hidden file. To show them, use the argument -a or -A:
"ls -A" or "ls -a"

Join the argument with -F
"ls -F -A" or "ls -FA"

Basic Unix/Linux File Permissions -Video-Watch Online



Contents
Basic Unix/Linux File Permissions
Understand the basic of Unix file permissions.These videos goes through:the concept of permissions,regular file permissions, symbolic format of permissions, binary format of permissions,octal format of permissions, the concept of inodes,directory permissions.

Mac Desktop Video tutorials-Watch Online for Free



Contents
The Mac Desktop tutorials consists of tutorial on the Mac OS X DOck,desktop folders,downloads,trash,smart folders,system preferences, finder window,sound preferences

Windows Basics Video tutorials-Watch Online for Free



Contents
Using Undo command,finding a lost file, organizing file,moving files,selecting multiple files,recovering files, windows explorer basics,keyboard shortcuts,finding recent documents

Learn Linux-Video-Watch Online for Free



Contents
What is Linux,Why Use Linux,Different Linux Versions,Choosing a Version,Mepis 6 System Requirements,Getting FTP software,Downloading Linux by FTP,Verifying MD5SUM,Getting Burning Software,Burning Your Linux CD,Running Linux LIVE CD,Repartitioning the Hard Drive,Installing Mepis Linux,The Grub Menu .
Running Windows,Running Linux,Setting Up Email,Set Up Instant Messenger,Using a Flash Drive,Using OpenOffice,Playing CDs,Single vs Double Clicking,Burner Software,Files and Folders,Linux Directory Structure,Config Files,Capture Screen Images,Changing the Desktop Look,Exploring Software,Install using Synaptic,Install a deb Package,Removing a Package,Mepislovers Forum,Mepis WIKI,Man Pages (or Manual),Install App + Menu Editor,Create Desktop Shortcuts,Kicker Panel,Sample Desktop Tweaking,Shut Down


Series of videos that walk you through what Linux is, how to get it, try it out in Live CD mode, install it as a dual-boot operating system with Windows, and how to use it, including how to set up the most common applications such as email and instant messaging.

The benefit of this demonstration video is that it is a real world recording that takes you through all the steps, so you can later follow along to try out Linux yourself as a Live CD. If you decide you want to install Linux as a dual-boot operating system with Windows, (meaning when your computer starts, you are presented with a menu choice to run Linux or Windows) you are shown how to install Linux.

Linux was installed for free using the steps performed in this video. Linux is all about choice, and the best way to decide if Linux is right for you, is to try it out.

Unix history-Video-Watch Online

History of Mac OS-Video -Watch Online

Introduction & History of Window OS-Video-Watch Online

How Computer Viruses Work-Video-Watch Online

What is Grid Computing?-Video-Watch Online



Introduction to Cluster computing -Video -Watch Online



This video about introduction to cluster computing,comparison of parallel & distributed computing and its applications

What is Workstation? -Video -Watch Online

What is an Operating System?-Video-Watch Online

Introduction to computer storage-Video -Watch Online


how a computer holds and saves data

What is Computer? - Video -Watch Online for Free



Describes what a computer is, and how it works, and what can be added to it.

What is internet? -Video -Watch Online for Free



This video describes about how to connect to internet,internet service providers,Introduction to worldwideweb.

How to setup LAN Local Area Networks -Video -Watch Online



Creating a local area network through ethenet and modems.

Computer Networks Basics -Video -Watch Online for Free



How a computer network is made and how one works.

Computer Keyboard & its functions - Video -Watch Online

Computer Internal and External drives -Video -Watch Online

Overview and functions of a computer System-Video

Overview and functions of a computer System-Video-Watch Online for Free


This video covers about Input and output devices,Storage devices: Hard Disk, Diskette, Magnetic Tape, RAID, ZIP devices, Digital Tape, CD-ROM, DVD, etc (capacity and access time),Main Circuit Board of a PC: Chips, Ports, Expansion Slots, etc.

Bioinformatics Video Lectures - Watch Online for Free

The table of contents contains bioinformatics video lectures,clips and animations.

Introduction to Bioinformatics

Introduction to Amino Acids - Video Lecture - Watch Online for Free

Part 1


Part 2

Introduction to Protein structure - Video Lecture -Watch Online for Free

Biochemistry: Nucleic Acids ,RNA & Protiens -Video Lecture -Watch Online for Free

Biochemistry: Molecules and Shapes -Video Lecture-Watch Online for free

Biology as a Science - Video Lecture - Watch Online for Free

Bioinformatics servers down - Get notified via email

You may come across several bioinformatics servers often go for essential maintenance or frequent updates.If you would like to notify when the server up or down, there are several useful web service like Ding its' up'.As the name suggest,it tells when your favorite website is up.



You can just paste your url of the specific website and your email address, you will be get notified when the website is up or down.

Pubmedfight - Compare author publication competitiveness

We know about Googlefight is a website that allows users to compare the number of search results by the google search engine for two given queries.People often use this for entertainment or for measuring of competitiveness.

What about a similar tool in a science? Here is a Pubmedfight, a French tool, with which you can compare authors by their number of publication in Pubmed.

Bimatics forum

What is BIMATICS?

BIMATICS - Bioinformatics Open Student Society is a non-profit interest group mainly for students who are interested and/or working in the bioinformatics/computational biology field for exchanging information, sharing ideas and knowledge, discussing opportunities.

BIMATICS is for the students to discuss the applications and implications of bioinformatic in new era of Science.

MOTTO: To bring awareness in recent trends in bioinformatics, to improve the working knowledge of Students and to help the aspiring students who want to make a career in Bioinformatics.

GROUP FOUNDER & CREATOR: SURESH KUMAR, PhD student (BIOINFORMATICS), University of Vienna, Vienna, Austria

website address: http://groups.yahoo.com/group/bimatics/

BIMATICS- Bioinformatics Open Student Society - MEMBERSHIP

a) BIMATICS membership is open to a student interested in Bioinformatics. You might be a student at any level. You should be willing to volunteer in the activities of BIMATICS when required.

b) Researchers and Scientists working on Bioinformatics/Computational Biology related problems or those are wanting to implement bioinformatics methodologies to compliment their current research and share with students in this group.

Membership: Membership is free.

Join BIMATICS: Click here to join-BIMATICS














Subscribe to BIMATICS-Bioinformatics Open Student Society







Suresh Kumar - Bioinformatician and Blogger at Bimatics

Suresh Kumar is a Bioinformatician & a blogger, presently pursuing PhD. in Bioinformatics at Univesity of Vienna.He holds a Undergradute degree in agricultural science and Masters degree in bioinformatics.When he was in Master degree he started bioinformaticsweb website which is recognised as top education resource.He is also started bioinformatics forum called bimatics group which is one of biggest group in bioinformatics for sharing & exchanging ideas in bioinformatics.



Bimatics blog is one of few bioinformatics blog in internet which covers topics in bioinformatics which servers as tech guide for students.

Bioinformatics scholarships

This section contains information about bioinformatics scholarships for higher studies

Bioinformatics trainings

The table of contents contains bioinformatics trainings, project work listings

Bioinformatics Jobs

The table of contents contains bioinformatics jobs advertisments

Bioinformatics conferences

The table of contents contains bioinformatics,systems biology, computational biology conferences,symposiums listing

Bioinformatics software/tools download

Bioinformatics software & tools download

Bioinformatics news,tips & tricks

The table of contents contains bioinformatics news, useful tips & tricks

Computer video tutorials

The table of contents contains basic computer video tutorials, programming tutorials, computer hardware.

Biology video lectures

The table of contents contains biology video lectures,clips and animations.

Introduction to Biology

Computer tutorials for biologist - Bioinformatics background studies

The table of contents contains computer tutorials essential for biologist.

Biology tutorials for Non-Biologist - Bioinformatics background studies

This table of contents contains basic molecular biology,cell biology tutorials essential for better understanding of bioinformatics

Bioinformatics tutorials for everyone

This table of contents contains bioinformatics tutorials covering from introduction, definitions,intermediate to advance level.

Genomic Revolution - Video Lecture


About this talk
Scientific discoveries, futurist Juan Enriquez notes, demand a shift in code, and our ability to thrive depends on our mastery of that code. Here, he applies this notion to the field of genomics.

About Speaker
Juan Enriquez is an authority on the economic and political impact of science. In his 2001 best-seller As the Future Catches You, he examines the profound changes that genomics and other life.

Basic Unix/Linux Commands for Bioinformatics


UNIX/LINUX Terminal
Unix/Linux OS has a terminal. A "terminal" is a way of typing commands to the computer.You can either open a terminal inside your graphical environment, or you can switch your whole screen to a terminal

To open a terminal in a graphical enivronment
1. Open up your menu. This is either the "red hat" or "F in a bubble" icon in the tray (at the top or bottom of the screen). (It might also be a little "foot," or possibly a little penguin.)
2. Under System Tools, click on Terminal. (In some versions of Fedora, it's under Accessories instead of System Tools.)

To switch your entire screen to a terminal, press Ctrl-Alt-F1. You can then switch between six different terminals, by using Alt-F1 through Alt-F6. Pressing Alt-F7 will bring you back to your graphical environment.

After opening terminal, we can type these commands

LINUX/UNIX COMMANDS
ls (list). Does a directory listing.
ls lists a directory in columns
ls -l gives a fuller listing including file permissions, size, date created
ls -al similar to the above but includes "dot" files

cd (change directory).
cd return to the home directory
cd .. move up one directory level
cd ../.. move up two directory levels
cd subdirectory move to subdirectory

cp (copy).
cp file1 file2 copy file1 to file2
cp file1 subdirectory copy file1 to subdirectory
cp file1 file2 directory copy file1 and file2 to directory

mv (move). Moves or renames one or more files.
mv file1 newname renames file1
mv directory newname renames directory
mv directory existing-directory moves directory to a subdirectory of target
mv file1 file2 directory move files to directory

mkdir (make directory).
mkdir subdirectory creates a subdirectory in the current directory

more. Lists files one screen at a time. Pressing the space bar dislays the
next screenful and pressing q or ctrl-c cancels the listing.
more filename

cat (catenate). Display, combine or append files.
cat file1 display file1
cat file1 file2 > file1and2 combines file1 and file2
cat file1 >> file2 append file1 to file2

chmod (change mode). Change file permissions.
chmod u+w file1 add write permission for the user to file1
chmod g+x file1 add execute permission for the group to file1
chmod o-r file1 remove read permission for the world from file1

man (manual). Display reference manual documentation for the specified command.
man chmod display manual information for the chmod command
man -K keyword shows all of the man pages that contain keyword

pwd (print working directory). The default setup on nun is to have the
system prompt display the current directory. This means that there isn't
much need to use the pwd command.

rm (remove). Deletes files. Never use rm * (it will delete all of your
files). rm filename will remove the specified file. There is no
undelete. Some files may be recoverable from backups.
rm filename deletes the file with the specified filename
rm -i filename deletes the file after prompting

rmdir (remove directory). Deletes empty directories.

passwd (password). Changes your password. We recommend password of two
three letter words connected with a punctuation symbol or a number.
passwd newpassword changes your password

exit Terminates a session.

Homologous Membrane Proteins Dataset for Membrane protein Homology Modelling


Homology Modelling is crucial procedure for structure based drug design when the experimental 3D-structure of the receptor is not available.Modelling of Membrane proteins requires extreme care and presistent validation due to difficulty in obtaining their 3D experimental structures.Although, recently there is increase in the number of crystal strucutre of membrane proteins,many structures having low resolution and high R factors exist in the PDB.However we can improve the accuracy of the model with sequence alignment. This requires manually compiled accurate membrane protein structure datasets.

HOMEP contains homologous membrane proteins dataset which grouped into 11 families of similar topologies accroding SCOP classification except beta-barrels.

These datasets can be used to generate sequence alignments or build models with homologous membrane proteins

Reference:
Forrest L.R., Tang C.L. and Honig B. "On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins" Biophysical Journal 91(2):508-17 2006

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