বায়োইনফরমেটিকস শিখবো কিভাবে?

পৃথিবীতে একটা সময় পর পর উৎপাদন পদ্ধতিতে পরিবর্তন আসে।  সভ্যতা কম খরচে, পরিবেশের কম ক্ষতি করে আরো বেশি উৎপাদনের পদ্ধতি খুঁজে বের করে প্রতিনিয়ত।  এই মুহূর্তে পৃথিবীতে এইরকম একটা পরিবর্তন চলছে।  গত শতাব্দী ছিলো পদার্থ আর রসায়নবিজ্ঞানের।  এখন পৃথিবীতে জয়জয়কার জৈবপ্রযুক্তির।  জৈবপ্রযুক্তির রাজপ্রাসাদের সদর দরজা হলো মলিকুলার বায়োলজি বা অনুপ্রাণবিজ্ঞান।  অণুপ্রাণবিজ্ঞান কাজ করে মূলত ডিএনএ, আরএনএ, প্রোটিন ইত্যাদি নিয়ে।  প্রতি ষোল মাসে এই তথ্য দ্বিগুণ হচ্ছে।  এই বিপুল পরিমানের তথ্য বিশ্লেষণের জন্য তাই ব্যবহৃত হচ্ছে তথ্যপ্রযুক্তি।  বায়োইনফরমেটিকস হলো জীববিজ্ঞানে তথ্যপ্রযুক্তির প্রয়োগ।  এটি একটি মাল্টিডিসিপ্লিনারি বিষয় যেখানে লাগে জীববিজ্ঞান, কম্পিউটার, এলগরিদম, গণিত, পরিসংখ্যান, রসায়ন, পদার্থবিজ্ঞান সহ বিভিন্ন আপাত পরস্পরবিরোধী জ্ঞান।

শিখবো কিভাবে
সবচাইতে ভালো চলমান কোন প্রজেক্টে অংশ নেয়া।  তাহলে একেবারে হাতেকলমে শেখা যায়। তবে বাংলাদেশে আগ্রহীদের জন্য এই সুযোগ যথেষ্ট দুর্লভ।  তখন উপায় ইন্টারনেট থেকে বায়োইনফরমেটিকসের যে কোন গবেষণাপত্র বেছে নিয়ে তা অনুসরণ ও অনুকরণ করে।  কোন গবেষণায় প্রাপ্ত ফলাফল আবার খুঁজে বের করা বা রিপ্রডিউস করা যথেষ্ট চ্যালেঞ্জের।  এক্ষেত্রে  আগ্রহীদের সুবিধা হলো বায়োইনফরমেটিকসের কাজ করতে একটি কম্পিউটার ও ইন্টারনেট লাইনই যথেষ্ট। অন্য কোন যন্ত্রপাতি ছাড়াই অনেকদূর এগিয়ে যাওয়া যায়।  ইন্টারনেটে অনেক বিখ্যাত বিখ্যাত ওপেনসোর্স সফটওয়ার আছে, সেগুলো ব্যবহার করা যায়।

যা যা লাগবে
আমি জীববিজ্ঞানে পড়াশুনা করেছি, আপনি হয়তো কম্পিউটারবিজ্ঞান কিংবা গণিত নিয়ে পড়ছেন।  খুব ভালো।  কিন্তু কোন ছাড় নেই, সবাইকে সব কিছু শিখতে হবে।  অন্তত ন্যূনতম একটুকু জ্ঞান থাকতে হবে।  আধুনিক গবেষণাগুলো শুধু একটি জ্ঞানের অঞ্চলে হয় না।  দরকার হয় বিভিন্ন বিষয়ের আন্তঃসম্পর্কের ধারণা।  তার মানে এই না ওই বিষয়গুলো সম্পর্কে চারবছরের অনার্স কোর্স করে আসতে হবে।  এভাবে আসলে কাজ করা সম্ভব হয় না।  বরং আমাদের যখন যেটা লাগে, সেটা আমরা জেনে নিতে পারি।  ইন্টারনেট আছে কি করতে?
হ্যাঁ, অনেক সফটওয়ার আপনাকে বায়োইনফরমটিকসের বিশ্লেষণ করে দেবে।  তারমানে এই না যে আপনি বায়োইনফরমেটিশিয়ান। যেমন কেউ মাইক্রোসফট ওয়ার্ডে টাইপ করতে পারে তার মানে এই না যে সে কম্পিউটারবিদ।
অনেক বড় বড় কথা না বলে বরং দেখা যাক একজন নিউরোসায়েন্টিস্ট কি বলছেন:

learn how to do your own data analysis. Know statistics well. Know at least some basic programming/scripting in Python, R, Matlab, etc. This will be of immense value in helping you get your research done efficiently and correctly, without needing to rely on other people’s code (and time and commitment). This will become more important as our field becomes more data driven.

প্রোগ্রামিং জানেন না? কোন ভয় নেই। আপনাকে ধাক্কা দিয়ে প্রোগ্রামিঙের সাগরে ফেলে দেয়া হবে … নিজ দায়িত্বে তখন পাইথন শিখে নেবেন। ও ভালো কথা, আমরা এখানে পাইথন ব্যবহার করছি। পাইথন সম্পর্কে বেশি কিছু বলার প্রয়োজন নেই, গুগল এই প্রোগ্রামে তৈরি। আমরা এখানে বায়োইনফরমেটিকস, প্রোগ্রামিং দুইটাই দেখবো। বোঝেন বা না বোঝেন, অন্তত প্রোগ্রাম শেলে কোডগুলো কপি করে দেখতে পারবেন কি হয়। পাইথন এতো সোজা যে শিখতে মাত্র কয়েক ঘন্টা লাগবে।

It's Bio-Bio-1 Again after Long Posting Pause / Hibernation of few Years

6th Jan, 2012 --- SBK Closed due to Annual Picnic, DU denied access

13th Jan, 2012 --- Almost all initial / key members away from Dhaka or very busy ... But the Teams have started to self-roll & sustain .... :-).... !!!!
--- Today we discussed focusing on 3 topics. Somen discussed on Phylogenetic Networking, Santonu on CpG island and Robiul on DNA-walk model. Todays meeting was very informative.

Friday, the 27th Jan, 2012 at the SBK
About 10 persons gathered in the session ... (Arafat / Labony, Pls correct my memory issues ... Pls write some more briefs here ....What did we discuss ...?)

Saturday, the 28th Jan, 2012 at the KAL Theater, BMB Dept, DU
Today we had our symbolic starting session of the Bio-Bio-1 Bioinformatics Study Circle Session at the
Professor Kamaluddin Ahmed (the founder of the Biochemistry Dept in 1957, later renamed BMB in 2001,
Dept of Bio-Chemistry and Molecular Biology) Lecture Theater. It was magical and indeed an honor for the whole Bio-Bio-1 TEAM !!

Prof. Zeba kindly inaugurated this informal but memorable event with her kind introduction... (who knows in the coming days may be all of us will feel proud and glorified globally bcz we gathered like this regularly and helping each other with the knowledge of Life...;-)... Zeba Apa is a great Bio-Bio-1 sponsor and wisdom contributing member .. She has been graciously hosting the tea & biscuits for ALL the participants (almost 20 in our very first day...;-)...pls correct me .. if I'm wrong here...

Zaman introduced Bio-Bio-1 Team, how and why it all started.. and where are we now.. etc..etc... (since it was mostly informal impromptu speech .... so writing more details may distort the actual lines here ... :-(.... in fact .. I'm being lazy also in typing that here ...;-)...

Saddam shared his personal passion about Biology since childhood and his Bioinformatics interest since 2001... (in fact, he is the most senior-Bioinformatics-passionate-member in our founding core Bio-Bio-1 TEAM ...;-)... He also described our ongoing Bio-Bio-1 Study Program with the participants... More here.. http://bio-bio-1.wikispaces.com/Bio-Bio-1+Study+Program+II

Labony started with her Bioinformatics intro PPT slides. Although the young Faiyaz could not derive much interest initially, but it was very lucid and has been getting richer since her first lecture.

Everybody also introduced each other in the middle of the session ... (bcz Zaman forgot to start with his own introduction ...:-(...;-)...

Bio-Bio-1's symbolic start in this very day in KAL might be a great way to celebrate the Saraswati Puja Festival (the Goddess of Knowledge and Wisdom) ..:-)..


Friday, the 3rd Feb, 2012 at the SBK
After the Saraswati Puja magic @ KAL, BMB, DU, this evening was also magical ... Only 4 of us (Arafat, Nion, Saddam, Zaman) gathered :-(...
Saddam was passionate and punctual as ever ... But only 2 of his PPDs "Python Programming Disciples" showed up ... ;-)...! The Great Arafat and the Brave Nion !!!..;-).. But the "Adda" with Chola-Muri was also quite entertaining and enlightening ... :-)... I thoroughly enjoyed Arafat's eloquent description of the several theories on the Evolution of Life on Earth... His Bangla translated word "জৈব ঝোল" (Bio-Soup) sounded very attractive ... (Although both Saddam and I initially misheard it as "জৈবজ হোল"...;-)...

Saddam explained his great PPT slides on the DNA Base-Stacking Energy & Propeller Twist Calculation design to both Arafat and Nion, so that they can start the Python coding based on that...


Saturday, the 4th Feb, 2012 at the KAL Theater, BMB Dept, DU
Surprise ! Surprise !!
For the last few years, it was mostly the Bio-Bio-1 founding core Team Members usually gathered on time (now-a-days @ 5 PM) and used to wait for the other participants to come ...

But today is a glorious exception ....!! After waiting almost 10-15 mins ... Sajib Sir called Zaman over mobile phone ... while Zaman was rushing to the KAL Theater room from Prof. Zeba's Lab... And there were more than 25 participants waiting for the Bio-Bio-1 session .... !!!

Zaman was exalted and started expressing his excitements ... He shared his meeting minutes with the BMB, DU Chairman where he told that the Bioinformatics passionate BMB / DU students were Bio-Bio-1's main attractions and the Teachers would be extra Bonus .... :-)... A Great new Bonus was the presence of Dr. A.H.M. Nurun Nabi Sir (Associate Professor, BMB, DU) besides the "usual suspects" Sajib Sir and Prof. Zeba Madam ...;-)...

Zaman introduced the Bio-Bio-1 Team, how we all can work together...the modus operandi etc .. etc...
Everybody also introduced each other while starting the session today, after Zaman introduced quite a bit about himself ...

Saddam introduced himself briefly this time.. :-(... He also talked about our ongoing Bio-Bio-1 Study Program with the participants... More here.. http://bio-bio-1.wikispaces.com/Bio-Bio-1+Study+Program+II

Saddam started with the Great Python Tutorial... Everybody seemed to enjoy the session quite well... Zaman took some time in the middle and shared his usual 9-components (5-Bio, 4-Informatics) feedback loop modeling diagram (taken from the Modeling & Bioinformatics Book, Chapter - 4) with the participants. He also shared the Radial Diagram of Systems Biology of the three major Sciences interactions : 1. Life Sciences (i.e. Biological Sciences), 2. Systems Sciences, 3. Information Sciences

Although I made a headcount of about 35 in our today's session ... but signature wise it came about 26 or so ... in fact now I remember I also didn't sign ... :-(...
Arafat / Saddam, .pls correct me .. if I'm wrong here... Pls also add more... if you want..

Refactoring Unnesessary Commenting.avi

What is Python and why python in Bioinformatics?

What is Python and why python in Bioinformatics?

Python is a general-purpose high-level programming language whose design philosophy emphasizes code readability. Python aims to combine "remarkable power with very clear syntax", and its standard library is large and comprehensive. Its use of indentation for block delimiters is unusual among popular programming languages.

Source: http://en.wikipedia.org/wiki/Python_(programming_language)

Because scientists have long relied on the open availability of each other's research results, it was only natural that they would turn to Open Source software when it came time to apply computer processes to the study of biological processes. One of the first Open Source languages to gain popularity among biologists was Perl. Perl gained a foothold in bioinformatics based on its strong text processing facilities, which were ideally suited to analyzing early sequence data. To its credit, Perl has a history of successful use in bioinformatics and is still a very useful tool for biological research.
In comparison to Perl, Python is a relative newcomer to bioinformatics, but is steadily gaining in popularity. A few of the reasons for this popularity are the:

• Readability of Python code
• Ability to development applications quickly
• Powerful standard library of functionality
• Scalability from very small to very large programs

The Python language was designed to be as simple and accessible as possible, without giving up any of the power needed to develop sophisticated applications. Python's clean, consistent syntax leaves it free from the subtleties and nuances that can make other languages difficult to learn and programs written in those languages difficult to comprehend.
Python's dynamic nature adds to its accessibility. For example, Python doesn't require you to declare variables before you use them, and the same variable can refer to objects of different types over the course of its existence. Python can be also be used interactively, allowing you to familiarize yourself with the language of any Python modules in an interactive session where each command produces immediate results.
Python also has excellent support for the object-oriented style of programming. The basic idea is that object-orientation often provides a better way to organize the data and functionality within your programs. As the data and analytical techniques used in bioinformatics have become more complex, the value of object-oriented language features has risen.
In addition, Python integrates well with systems written in other languages, such as C, C++, Java and Fortran. One of the main benefits of C is speed. When a programmer needs an algorithm to run as fast as possible, they can code it in C or C++ and make it available to Python as an extension module. To the programmer, these are indistinguishable from pure Python modules. Similar utilities exist that make the large body of scientific algorithms coded in Fortran accessible to Python programs.
Java has become popular as a cross-platform and Web development language. The Python interpreter is now available in two variations: one version written in C, and the other version, known as Jython, written in Java. Jython allows Java programmers to write programs using the Python syntax and dynamic language features, and it allows Python programmers to use existing code developed in Java. These are just a few examples of the many ways Python is able to leverage and extend existing code written in other languages.
So while Perl is more well established in the bioinformatics community, many biologists and bioinformaticians are also turning to Python as it gains in popularity.

Source:

Beginning Python for Bioinformatics

by Patrick O'Brien

http://onlamp.com/pub/a/python/2002/10/17/biopython.html

you can download this from :
http://groups.google.com/group/bio-bio-1/files?upload=1

Interesting Books on BioInformatics

http://biowww.net/biobooks_1_sequence-analysis.html


Courses in the South Korean University .....
http://bi.snu.ac.kr/Courses/bio02/bio02_2.html


South Korea is doing great in R&D in BioInformatics....

Some Helpful and Interesting Links on DNA

DNA Key to life

http://www.youtube.com/watch?v=cwfO6SzGaEg&feature=fvw

Dna Lab part 2

http://www.youtube.com/watch?v=iyb7fwduuGM&feature=fvst

DNA: From The beginning

http://www.dnaftb.org

Some Important Links of Cell Biology

I think understanding bioinformatics depends on the concepts of cell biology (cell anatomy, cell function, chromosome structure, etc.. ). So, here i provide some important links from where you can get the concept of cell biology :

http://www.johnkyrk.com/index.html
http://www.biology-online.org/1/1_cell.htm

If anyone interested on "Origins of Life on Earth"

http://www.biology-online.org/10/1_first_life.htm

Future i will discuss the hot topics of cell biology which need to understand Basic Bioinformatics.