How to resolve conflict in Science: On FMDV classification problem

How a scholarly conflict on FMD virus classification between Bangladeshi and Chinese research-groups was resolved.

Scientists form hypothesis, formulate experiments and publish their results. But not all researchers agree to the same conclusion. Hence, comes scientific-conflict. How to resolve that? Publish and exchange opinions!

Recently, scientific debate and exchange of opinions came to my attention. Back in Bangladesh during and after my MS study in Microbiology at the University of Dhaka, I was affiliated with Dr. M Anwar Hossain’s FMDV research project (Microbial Genetics and Bioinformatics Lab). In that project, Dr. Hossain lead the research on Foot-and-Mouth disease virus detection and vaccine development. Briefly speaking, this is a very dangerous viral disease of cattle and cause several million dollar loss in agro-veterinary economy in Bangladesh.

Figere 3 from Siddique et al. 2018 shows that proposed sub-lineage Ind2001BD1 and BD2 do not fall into established genotypes. Source: https://onlinelibrary.wiley.com/doi/epdf/10.1111/tbed.12834

The FMD is an RNA-virus and it evolves very fast due to higher mutational rate. Classifying newly emerged FMD virus can be a complex task. I co-authored a paper (Siddique et al. 2018) on which the research group detected two novel sub-lineage of FMDV virus, namely Ind2001BD1 and BD2. We have used distance-based clustering method (multi-dimensional clustering: novel in this field but widely used for classification) as well as more traditional phylogenetic method to establish and propose this. In this point, I should mention that there is a world reference laboratory for FMDV characterization (WRLFMD), but FMDV strains isolated by Siddique et al. 2018 did not fall into the classification maintained by them.

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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.]

 

writing

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-couse (MOOC) Coursera.org has pretty good materials (video+tutorial). One can download the course materials from this Google drive folder.

2. On Shikkhok.com, 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.

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Optical Density Hack: Use Visual Comparator in Antibiogram

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.

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. Continue reading “Optical Density Hack: Use Visual Comparator in Antibiogram”