Note for First-Year Graduate Student

Few tips for new graduate-students to make shift from undergrad mindset to become an independent researcher.

The Bell Tower, University of California, Riverside

If you are a new graduate student, time can be tough because you have a lot of hassles in the first year. You have several heavy coursework, need to maintain minimum GPA, have to do teaching assistants (TA),  probably rotate in labs and select your Ph.D. supervisor, learn new skills in the laboratory as well as set-up yourself in a new city (new country for international students like me), explore the new campus, make new friends and cook your own food. That’s a lot for the first year.

While it is easy to become overwhelmed to meet these requirements, a fresh graduate student must not forget the big idea of a Ph.D. research. Many new graduate students are fresh Bachelor or Masters degree holders who approach the Ph.D. program as like undergraduate school, which is a mistake. Often there can be a gap of suggestion and lake of help to make a clear conception of what a Ph.D. program is.

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Statement of Purpose

[This is a writeup from 2016. Caution! If you are willing to apply in US for higher study and planning to write SOP soon, I’ll suggest not to read this write-up, because it may bias you. And do not use this format as your SOP. Your SOP is supposed to be unique. Better, write your own SOP, then show it some experienced for valued feedback.]



When I was a student of class 9 in secondary school, for the first time I participated national science fair with an electronics project “Determination of gravitational acceleration constant g using digital method” as a member of science club Anushandhitshu Chokro. It was awarded the 1st prize in district level and 8th in national level. From that moment my inspiration in science started to flourish, which is one of the motivating factors for why right now I want to enroll a Ph.D. program to get a rigorous training of scientific method. Continue reading “Statement of Purpose”

Show Your Work

Show Your Work

Sometimes we are practitioner of a field, professionals or artists do not feel easy to show our own work, the process of work, what we are learning, sharing our work with more general people. This book encourage and provide some guidelines for that, because time has been changed in this connected world. Key suggestions are to show work regularly, keep a good (domain) name, teach people what you are learning, creating a cult of followers along with following and being part of practitioner community. Very small book.

By Austin Kleon


Python for Bioinformatics: An Online Course from Me!

I teach an on-line course ‘Python/Biopython for Bioinformatics’ in cBLAST. This is three month’s course, I use biological examples showing how we use Python to handle and analyze biological data. The video lectures are in Bangla, and video’s are both slides and screen-casts of coding.

Center for Bioinformatics Learning Advancement and Systematic Training, or cBLAST, is part of University of Dhaka, Bangladesh. One will get certificate after successfully completing this 3-month course for University of Dhaka.

Python, is an easy-to learn, high-level computer language that is used in many of the computational analysis in Bioinformatics.  This course will start developing initial skills of interactive programming and script writing in Python. Then we’ll cover Biopython, Matplotlib and NumPy. Finally, some algorithmic aspects of programming will be discussed in this course. Continue reading “Python for Bioinformatics: An Online Course from Me!”

A note on learning computational biology

Many asks me about learning Bioinformatics. So, I’m going to put some good learning resources in this note.

If you are a complete beginner, don’t aim to ‘understand’ everything discussed in a course or lecture or book. It’s okay to be partially ignorant but still moving forward. Try to go through 60-70% content of the following source within one-two months. The objective in this stage is to get some good understanding of core Bioinformatics concepts and terminology.

Complete Beginner

1. Bioinformatics Methods I and II, offered by Toronto University in massive-open-online-course (MOOC) has pretty good materials (video+tutorial).

2. On, a MOOC platform in Bengali language, there is a very short course on Bioinformatics, বায়োইনফরমেটিক্স পরিচিতি, offered by Bio-Bio-1 Foundation.

3. Reading books is the best way. I’ve found ‘Essential Bioinformatics’ by Jin Xiong an easy to understand book.

Continue reading “A note on learning computational biology”

How to use McFarland solution to visually compare bacterial culture

Say you have a bacterial isolate and you need to check its antibiotic resistance profile. In this case, you need to do an antibiogram study. Ideally, you’ll need to make bacterial lawn on Mueller-Hinton agar medium for doing antibiogram. For that purpose, you prepare bacterial culture from stock in nutrient broth and place it in shaking-incubator. When the culture is young enough, that means when the bacteria on the beginning of its growth phase, you use the culture to make lawn on Mueller-Hinton agar plate. How do you know the culture is young? The common practice is to measure its spectrophotometric absorbance at 600nm. If the culture’s optical density or OD is near to 0.1, then it is perfect for making a lawn. Very simple procedure.

McFarland standards. No. 0.5, 1 and 2. Source Wikipedia.

But this can be a cumbersome job when you have to handle many bacterial cultures rather than one. If bacterial samples you are working with are of different species, then their binary fission time will vary. For some bacteria cell division rate is higher and it’s culture will approach to 0.1 OD fast. For other, the rate will be slow and thereby their culture will take time to get that point.

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এতোই দক্ষ যে উপেক্ষা করা অসম্ভব

So Good They Can't Ignore You: Why Skills Trump Passion in the Quest for Work You LoveSo Good They Can’t Ignore You: Why Skills Trump Passion in the Quest for Work You Love by Cal Newport

“Compelling careers often have complex origins that reject the simple idea that all you have to do is follow your passion…”

কাল নিউপোর্ট MIT থেকে গণকযন্তরবিদ্যায় পিএইচডি করা লোক; উনার স্টাডি হ্যাক ব্লগটা ( মাঝে মাঝে দেখা হয়। মনের মতো কাজ কিভাবে খুঁজে নিতে হয় এ বিষয়ে বইটি লেখা। প্রথমেই উনি passion-কে বাতিল করে দিয়েছেন 😮 । তার মূল কথা এমন সব গুণ অর্জন করতে হবে যেগুলো দূর্লভ কিন্তু দরকারী, তাহলেই নিজের পেশাকে passion-এ পরিণত করা যাবে। এজন্য শিল্পী বা দাবাড়ুদের মতো deliberate practice-র পক্ষপাতী তিনি। বইটা ভালো লাগলো, কারণ বইটা knowledge-worker-এর পরিপ্রেক্ষিতে লেখা। সাধারণত দাবা কিংবা সংগীত ইত্যাদি পারফরমেন্স নির্ভর পেশায় ভালো করতে গেলে কি ধরণের চর্চা লাগবে তার সুপ্রতিষ্ঠিত নির্দেশনা থাকলেও জ্ঞানভিত্তিক কাজে নিয়োজিতদের জন্য এ ধরণের ভালো নির্দেশনা দূর্লভ।


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সহজ বাংলায় (ইংরেজিতে :p ) পরিসংখ্যান

Statistics in Plain English, Third EditionStatistics in Plain English, Third Edition by Timothy C. Urdan

রেটিং: ৪/৫

বিশ্ববিদ্যালয়ের প্রথম ও দ্বিতীয় বর্ষে পরিসংখ্যান পাঠ্যহিসেবে থাকলেও তা মাথার ভেতর খুব একটা ঢুকতে পারে নি। একাডেমিকভাবে পরিসংখ্যানের ক্লাসগুলো ছিলো গণিত-ভিত্তিক, সূত্র আছে অংক করো এই ধরনের। গণিত দরকারী জিনিস, কোন ধারণাকে বিমূর্তভাবে উপস্থাপনের জন্য অপরিহার্য। তবে পরিসংখ্যানের আলোচ্য বিষয়গুলো আসলে কোন প্রেক্ষিতে কি দরকারে এসেছে, প্রতিটি বিষয়ের গণিতের পেছনে ভাবনাটা আসলে কি এই অন্তর্দৃষ্টি তৈরি না হলে আলোচনাগুলো অর্থহীন হয়ে পড়ে। তখন শুধু সূত্র শিখে অংক কষাই হয়, পরিসংখ্যানের কোন বোধ তৈরি হয় না। পরিসংখ্যান না বোঝার কারণে পরবর্তীতে থিসিস করতে গিয়ে কিংবা কোন বৈজ্ঞানিক নিবন্ধ পড়তে গিয়ে ঠেকে যেতে হয়েছে। এরকম অবস্থায় স্ট্যাটিস্টিকস ইন প্লেইন ইংলিশ বইটা হাতে আসে। এখানে লেখক পরিসংখ্যানকে গাণিতিকভাবে উপস্থাপনের চেয়ে কোন বিশ্লেষণ পদ্ধতি কোন প্রয়োজনে এসেছে, পদ্ধতিটার মানে কি দাঁড়ায়, বিশ্লেষণের পেছনে অন্তর্দৃষ্টিটা কি এই বিষয়গুলোতে বিস্তারিত আলোচনা করেছেন — সোজা বাংলায় (মানে ভাষাটা ইংরেজী হলেও আলোচনাটা সরল ভাষায়)। এই বইটা পড়ার পর পরিসংখ্যানের অনেকগুলো গুরুত্বপূর্ণ আর প্রাথমিক বিশ্লেষণ পদ্ধতির ধারণা পরিস্কার হয়েছে আমার। পরিসংখ্যানের আরেকটু সিরিয়াস বুঝ্ তৈরি করতে এই বোধ্-টা কাজে দেবে।

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অতীতের আলো

ধূলি আর ধোঁয়ার কুয়াশায় মলিন আকাশটা
শহুরে আলোর হট্টগোলে জর্জরিত হয়তো –
কৃষ্ণপক্ষের ফালি চাঁদটা সরে গেছে
আকাশের একপাশে।
উদ্ধত টাওয়ারের মাথায়
লাল আলো – নাকি লোহিত বামন তারা সে এক?
ভ্রম হয়-

তবু একাকী উজ্জ্বলতায় একটি নক্ষত্র হয়তো চোখে পড়ে।
শরতের দক্ষিণ আকাশে।

তার এই আলোর যাত্রা শুরু হয়েছিলো
কত লক্ষ বছর আগে?
পৃথিবীতে হয়তো তখন নিয়ন্ডারথাল মানবের বিচরণ।
তাদের আকাশ চিরে ছায়াপথের দুধেল ধারা
আর তারা নিয়ে কত বিস্ময় কল্পনা।
শিকারী কালপুরুষ, বৃহৎ ভল্লুক আর সিংহের
গভীর অরণ্য হয়ে যায় আকাশটা।
আরো কত ছবি ঐ আকাশের অবতল ক্যানভাসে
অবলীলাক্রমে সহজ সরলতায় সৃষ্টি করে চলেছে।

সেই নিয়ন্ডারথাল পিতার চোয়ালের ফসিল হাতে,
আমি আকাশে একটি উজ্বল তারা দেখি
সে তারা নিয়ে আসে অতীতের আলো।

State of traffic-jam in Dhaka during political instability, 2015

The year 2015 started with acute political crisis in Bangladesh. One of the major political party, BNP, called for an endless blockage until or unless present government leading by AL leave their power and another national election get organized. As the method of political block, BNP organized terrorist ambush activities such as petrol bomb attack in public buses. Many people died due to massive burn, many are still fighting against death, and death toll gone wild day-after-day. In that time, everyone was in horror. There was a sharp decline in transport by bus. Me along with my father also started avoiding bus-ride. In this situation, I noticed an unexpected scenario, there was no traffic-jam in the roads of Dhaka.

This observation worth telling. As the blockage was continued for indefinite time, offices and business did not halted their activities. So every earning member of all family had to work during day. Although many of the citizen of Dhaka have private-car, they did not bring it out of garage due to safety: who knows when a petrol-bomb will burn the car in public-place! As many of the people started avoiding public-bus services, rickshaw-ride increased. Almost all VIP roads, where rickshaws were not permitted in normal time, were open for rickshaw. What I observed in that turbulent time that there was no traffic jam in prime hours! It’s not the case that those one have job or business just halted working during the blockage, but they stopped using private-car. Almost no private-car on the roads, everyone travelling through rickshaw, and no traffic jam! This was the common scene during the first-months of the political blockage. I shared the view with other peers and they confirmed this with similar observations.

Traffic-jam is an irritating problem in Dhaka which kills around one to three hours per day in average in my daily-life. Government is apparently trying to solve this problem by constructing new fly-over bridges, expanding width of existing roads, making new-one, building elevated high-ways but the problem seems is not as easy to solve. Although lot of private car is not the only element of traffic-problem is Dhaka and there are other elements of the problem that worth analyzing. But above observation indicates that decreasing the use of private-car may provide a feasible solution of a long existing problem. I think many might cry at me that private-cars are not the root-cause but disobeying the traffic-rules is. This claim also hold some truth, in fact almost none of our drivers follow any traffic rules that are related with vehicle-mobility, rather they follow jungle-laws that has been emerged from the extreme-load of transport vehicle in roads. This load of transport vehicle is so high in Dhaka in office-times that its not possible for a traffic surgeon to employ traffic-rules. I have some observation in other facets of this critical problems and will share my opinion in this blog soon.