The blog hits 153 in one month

Ever since I put up the visitor location hit counter a month ago. I have been watching the number of visitors go up beyond my expectation. There has been 153 hits for the past month (an average of 5 visits per day). :-) Very encouraging to me. I wonder if most of the hits come from Pulau Redang and Taman Negara posts. I do hope that the readers can post more comments on the reviews I wrote because I'm not always right. Thanks again for visiting.

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Seminar on GM crops public awareness

Date: 28 May 2009 (Thurs)
Time: 8.30 AM - 12 PM
Venue: MTBIC Hall, MARDI, Serdang
Speakers from UTAR, MABIC and MNRE.
4 papers will be presented:

• GM Crops: A Springboard for Agricultural Advances
• Public Perception on GM Crops: The Fear of the Unknown
• The Malaysian Biosafety Act 2007
• The Obligations of Researchers Under the Malaysian Biosafety Act 2007

After lunch, there will be book launching event of “GLOBAL STATUS OF COMMERCIALIZED BIOTECH/ GM CROPS: 2008” and a keynote address by Dr. Randy Hautea from ISAAA on Global Status of Commercialized GM Crops in 2008.

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Biotechnology research position in Malaysia: Where to look?

If you have decided Research is right for you, the next step is to look for a research position. With a first degree, you can either choose to work as a Research Assistant (RA) or continue postgrad studies. Either way you will need to contact the university or the research institute to find out if there's any vacancy.

This information will not be showed on the their official websites.You are definitely not going to find it in the newspaper. Job search website just keep sending you unrelated jobs. Attending a career fair is not going to help much.

The problem with biotechnology related job vacancy is it is often spread by word of mouth. Someone you know might send you an email saying they are looking for a RA and ask you to forward this message to people you know. Sometimes, a sales representative come in the lab and ask if anyone interested to join their company. The information is not readily available to others because they think that recommendation enables better selection of candidate.

So the best way to start is still checking the websites of university and research institute. Look through the list of researchers and their projects. Shortlist those who you are interested to work with. Send an email to ask if they have any vacancies. Remember, it doesn't cost anything to try. Timing is crucial and the position available is limited. The team might not have any extra projects at the moment. If so, you should ask if they know someone else who can offer a job. Be sure to contact them a few months before you graduate.

It's good to stay in touch with your supervisor or staff you work with during industrial training. They will inform you if there's any position available. If they have a good impression of you, they might offer you a job. Therefore, I strongly recommend students to attend internship although it's not compulsory for certain universities.

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Biotechnology career in Malaysia

Occasionally someone will call me to ask about the career options in Biotechnology. It's usually this time of the year as most undergrad students are finishing their final exam. I will ask them if they want to continue their studies to postgrad level. If yes, I will give some advices based on my own experience.

Basically, I think there are only three types of job in science: Lecture, Research or Sales. Those jobs that didn't fall into these categories are the minority. Meanwhile, some took off after realizing biotechnology is no longer what they want to do.

Lecturer is a profession that requires high academic qualification. "Are you going to become a lecturer?" is the most frequent question asked to a postgrad student. A master degree is not sufficient to get you into a local university with ranking. If you are not tired of writing proposal, teaching lecture, writing papers/publications and little time to conduct research, then welcome to the world of Academic.

Next, if you prefer spending your time in the lab and publishing your results. Don't forget the rule: if you don't publish, your research never exist. Option 1: Take up a research positions at university or institute. If you think you have gain enough research experience and you want higher salary, go to option 2: Join a private company research facility.

By now, you should have finally realized that there's no way a Biotechnologist can be rich. If you still have that dream, you might consider Sales as an option. A basic degree in science is required. Sales representative is the one who introduce and sell products to the researchers. Everything from chemical, kit, lab equipment and other services. They come to the lab on a regular basis so that we don't forget them. We hate sales person who don't reply us or being rude. So, service with a smile! This job pays off well if you are a good sales person and your products are selling.

There are some jobs related to management and consultant that requires background in Biotechnology. I'm not going into that. Whatever path you choose, remember LIKE WHAT YOU DO not do what you like!

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DAAD Postgrad Scholarships on Forestry

The German Academic Exchange Service (DAAD) offers scholarships for post-graduate studies and research to Malaysian nationals for the academic year 2010/2011. The courses available are in the field of Business, engineering, mathematics, veterinary, sociology, education, Agricultural and Forest Sciences.

Click here to view the list of courses. Visit DAADKL website for more information.

Not every year DAAD scholarships are open to Malaysian students. This is a great opportunity! And look... there's two courses on tropical forestry!!! If only last year I have this opportunity. Ich möchte in Deutschland studieren *sob *sob

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Seminars on HEV, Hepatitis B and influenza

A series of seminars on HEV, Hepatitis B and influenza will be held this week by the School of Biosciences and Biotechnology (PPBsBt) and Malaysia Society of Applied Biology (MAB). The invited speaker is Prof. Dr. Jungsuh Park Kim from Korea University. All are invited.

Title: HEV discovery and beyond
Date: 21 May 2009 (Thurs)
Time: 2.30 pm - 4.00 pm
Venue: Bangunan Biologi FST UKM

Title: Hepatitis C virus drug discovery
Date: 22 May 2009 (Fri)
Time: 9.00 pagi Venue: G143, Bangunan Biologi FST UKM

Title: Influenza: old and new threats
Date: 22 May 2009 (Fri)
Time: 3.00 pm - 5.00 pm
Venue: G143, Bangunan Biologi FST UKM

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Plant Genome Sequencing

I have always wanted to write a post on this topic. Last week, Iattended an informal talk on oil palm genomics. On the same week, Sime Darby announced that they have completed oil palm genome sequencing. This means that another private company has completely sequenced the most important crop in Malaysia. A few years back, there was a debate of whether Malaysia should sequence this plant. Many people don't see the importance to sequence this crop. But, we can understand why.

One major problem in plant genome sequencing is high cost. The sequencing projects are usually joint-collaboration from several sequencing centers, research institutes and universities research groups. Together, they formed a consortium and held meetings on regular basis. Most of the time, one group will be in charge of sequencing one or more chromosomes. Priority will be given to chromosomes that are known to possess desired traits or have most genic region. The difficulties of plant genome sequencing lies in the complexity and large genome size. Some plants are polypoidy. Plant genomes consists a lot of repetitive elements that can be hard to resolved.

The main goal of a plant genome sequencing project is often crop improvement (with the exception of model crops). The first three years involves genome sequencing, assembly and annotation. Re-sequencing and finishing efforts can take a few more years. After the genome is completed, 3 years are required to develop Marker-Assisted Selection (MAS) using high throughput markers such as SNPs. Association mapping and QTL mapping can be carried. The timeframe from genome sequencing to successful phenotypic selection can take at least 9 years.

Joint Genome Institute under US Department of Energy has been actively involved in many sequencing projects. JGI community sequencing programme offers genome sequencing grants . The organism sequenced must be related to energy issues. Basically, this rule is applicable to all microbes and plants because they can produce biomass... which can be converted to biofuel. The catch? Every project must involve US collaborator.

So where does the future lies with researchers from developing countries who can't afford to sequence the whole genome? Here's my suggestion: use a related species as your reference genome. Publications using EST will give you some ideas how genomic studies were carried out in the past. So, keep working with the Poor Man's genome until... genome sequencing become much more affordable.

Complete Genomics has targeted $1000 for a human genome (3.2Gb) this year. That is a few times the size of most crops (Bear in mind that oil palm is 1.8Gb). Whether they can achieve that is another issue. The thing is...Next Generation Sequencing is transforming genomics at a fast pace now. How far is $1000 plant genome from now?

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Ranting about submission deadline

Oh man, I'm sitting here now at Taipan's Station1 Cafe because I want to use WIFI to submit an abstract. I had to do it before midnight and then...the submission deadline is postponed to 10 days later!!!

I was like What!!! The deadline is still the same when I checked it 6 hours ago. Why didn't they put it up at the website earlier! Geramnya. I should have guessed that most conferences like to do that. Well, I'm glad I have more time to do correction.

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Advanced instrument the key to productivity?

Last week is the first time I was introduced to FlashGel. In case you didn't know, FlashGel is a gel electrophoresis set that is extremely fast and EtBr free. It has been out for awhile now but I didn't notice it until the sales representative gave me a brochure. My first reaction is "Hey, I saw this on a blog yesterday. They are teaching school kids in US how to use it."

Imagine if I don't have to prepare agarose gel (~30 min), run DNA for an hour, strain and destrain gel (~20 min) and capture gel photo using a imager (~10 min). I could save 2 hour each day assuming I only need to run a gel per day. While it's true that the lastest instrument can really speed things up, we usually don't buy them due to pratical use. My colleague recently visited a renowned research institute and was shocked to find that some facilities are under-utilized.

After that, I had a conversion with my other colleague discussing the productivity in our lab compared to the labs in well-established institutes. While students here have to do everything from A-Z, over there technicians are employed to perform basic tasks such as filling the tips, running PCR and running gel. That explains how a thesis is completed in a short time. But as a student, I would rather do all the work myself.

Not every problem can be solved with the current technology. Given a situation like this: you need to extract DNA from 4000 samples, run 96 well plate PCR and do fragment analysis. Even with 96 well tissue lyser, you need to perform DNA extraction for 40 times! Plus, you must have a really sharp memory and make no mistake. The best solution in this case is still REDUCE SAMPLES!

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Have you apply Toray Science Fund?

Malaysia Toray Science Foundation

Don't tell me you don't know! The Poster was up at Bangunan Biologi main entrance since Jan this year!

MTSF's research grants is open for application each year. It provides total grants up to RM300,000. Qualified young scientists (including postgrad students) are encouraged to compete for the Science and Technology Research Grant. Based on past awards, all recipients received a minimum of RM20,000. Shortlisted candidate will be called for interview. Submission deathline is 31 May 2009.

So don't miss out on this opportunity! Click here for more info.

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Merck Young Scientist Award 2009

You can become the next Merck Malaysian Young Scientist 2009. 3 prizes for each category up for grabs. 1st prize winner will receive RM 5,000 cold hard CASH!!!... and a trophy.

Eligiblity:

• Malaysian citizen;
• Postgrad student in Malaysia Universities in 2007/2008;
• Publications/papers published in a scientific journal in 2008 for Biosciences and Chromatography.

Deadline: 30 June 2009

Click here for full details

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Some recent thoughts (April 09)

Ta da! Finally, I got a new laptop! (Wait, no picture?!) Ever since my 3-year-old laptop met its worst enermy (water!), I have been borrowing sister's laptop. I spent almost a whole day installing softwares and updates. Now it's running smoothly. To my suprise, I don't feel any difference in running 64-bit Vista. I hope to run some data analysis with my new baby. Gotta start using Linux soon.

And a bit more on SOLiD... This week two SOLiD application specialists paid a visit to my lab. They are eager to assist SOLiD users in data analysis and publications. We definitely don't see others offering the same assistance. NGS is always evolving and very soon what we are doing now is outdated tomorrow. It's important to publish a paper FAST.

I just attended a scholarship interview yesterday. Only 5 mins is given for the presentation. The interview is over in a blink of an eye. I'm gonna stay positive whatever the outcome is. *Jason Mraz singing Make It Mine in the background*

The weather is so hot lately. I can feel the heat in the evening. Two weeks ago I visited a forest plantation in Johor. Here's what our fellow FRIM forester thinks about the weather:

”No comment"

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ABI SOLiD softwares: SOLiD Bioinformatics Workshop Part III

During the workshop, Dr. Sun presented some unpublished data on de novo genome assembly of rice blast fungus with a size ~40Mb. Partek Genomic Suite which is a third party software that can handle SOLiD data has been demonstrated. Generally, it performs gene expression analysis. It can run on all OS and requires minimum RAM.

We were then introduced to SOLiD Software Community. SOLiD suers can download a variety of data analysis tools from http://solidsoftwaretools.com for free. Tools available includes secondary and tertiary analysis softwares. Datasets such as human small RNA, whole transcriptome, E.coli single reads and PE reads can be found in that website. I got a chance to play around with SOLiD de novo assembly tool using E.coli dataset. The software is user friendly. I imagined working with color space is a very complicated task but it's easier than I expected. This software automatically display base read after assembly. There is a Find option to locate the reads which I find pretty useful. Another advantage is that the softwares can be installed on all types of OS (which is great for Windows user like me). Click here to read application note on SOLiD software suite.

Here's a list of other SOLiD softwares
• Academic and open source - Velvet, MAQ, SOCS, Bowtie, BFAST, SHRiMP, PASS
• commercial softwares - NextGENe, CLC Bio, ZOOM, Partek
(Most resources come from seqanswers.com and lh3)


Related posts:
SOLiD Bioinformatics Part I : Introduction
SOLiD Bioinformatics Part II: de novo assembly

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MGI Seminar on multiplex quantitative expression studies

A novel multiplex solution for quantitative expression analysis
Date: 13 May 2009 (Wednesday)
Time: 10.00 am – 12.30 pm
Venue: Nucleus Block, UKM-MTDC Technology Centre (Malaysia Genome Institute/MGI)
Speaker: Ms Rachel Wang, Application Specialist, Beckman Coulter, Singapore

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