Summary: Career talk by Biotech Corp

Here's the summary of the Biotechnology career talk given by Biotech Corp since not many people attend it just now. The important things to note:

• BiotechCorp is providing training for fresh Biotech graduates through BeST programme (Biotechnology entrepreneurship Special Training) to prepare them for the biotech industry. This training which combines training (obviously!), lab work and industrial internship will last for 3 months. Wow... super-intensive! The trainees will be given a monthly allowance of RM1000 (Rub my eyes again!). There are 3 intakes: April/May, August and December.
  
• Besides that, BiotechCorp also offers internship and incubation programme. Incubation Programme is aimed to help young biotech entrepreneurs.
• A biotechnology career fair is coming soon. It's known as BioCareer Fair & Exhibition and will be held in KL Convention Centre from 25-26 April 2009
  

Read more...

The Next Generation Sequencing Status in Malaysia

Since the introduction of Next Generation Sequencing (NGS) in 2005, the science community in Malaysia has been increasingly aware of it due to the rapid development of NGS technology in various applications. Here are the major local players in Malaysia’s NGS field to look out for:

Synamatix Sdn. Bhd. It is the most experienced company in NGS bioinformatics. It is founded in 2002. Synamatix has successfully established itself overseas with the introduction of SXoligoSearch. This software will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Synamatix also provides outsourcing NGS service. MGRC, a wholly-owned subsidiary of Synamatix Sdn Bhd. has been actively engaging in talks with potential NGS users and conducting NGS-related seminar and workshop.

Novocraft Technologies Sdn. Bhd. It is another Malaysia-based software company that has gained BioNexus status recently. Its product Novoalign is a fast and efficient tool for Illumina Solexa reads. Unlike SXoligoSearch, Novoalign is free for academic and non-profit use. The company is the official vendor in Malaysia for Cofactor Genomics. Cofactor Genomics is a US-based company that offers Illumina Solexa Seqeuncing. Besides cheaper and better quality of sequencing, it offers transparency in sequencing price and sample queue to its customers.

Two other companies are Science Vision Sdn. Bhd. and Analisa Resources Sdn. Bhd., the official representative for Illumina and Applied Biosystems respectively. Both have something in common. Besides organizing NGS-related seminar and workshop and offering sequencing service via outsourcing, they work closely with their Singaporean counterparts.

After so much talk and expectation, the first NGS platform has finally landed in Malaysia! UiTM has bought one unit of Illumina GAII. I'm sure the local researchers will be looking forward to cheaper Solexa sequencing from UiTM.

Read more...

Next Generation Sequencing: Era of short reads

I thought that I should do a brief introduction on Next Generation Sequencing (NGS) before my next post.

Next Generation Sequencing is, as the name infers, a new DNA sequencing technology compared to the traditional sequencing (Sanger sequencing).When people ask me what’s the difference between NGS and Sanger, I’ll say no cloning, cheaper, higher accuracy, higher throughput in one breath! However, NGS produce shorter reads compared to Sanger sequencing.

The NGS platforms that are currently running in the labs are 454 GS-FLX Titanium (replacing GS-FLX), Illumina Solexa GAII (Will be replaced by GAIIx) and ABI SOLiD 3. 454 sequencing is the only NGS technology that can sequence up to 400bp but it has lower throughput compared to the rest (180Mb/run for GS-FLX Titanium). Both Solexa and SOLiD is expected to achieve 100bp in length and up to 10 Gb/run this year. Among the applications of NGS are whole genome sequencing, transcriptome sequencing, gene expression (RNA-seq), microRNA, Chip-Seq etc.

Despite all the advantages of NGS technology, the main challenge when handling short reads is bioinformatics. The assembly of short reads will produce more contigs due to repeats problem. Again don't want to elaborate on that.

I would recommend this paper by Elaine Mardis. It’s a very comprehensive review on NGS. Please bear in mind that most paper in 2006 will compare Sanger and 454 sequencing. After the emergence of Illumina Solexa and ABI SOLiD in 2007, the papers would compare all 3 platforms. For those who are interested to know more about the challenges of NGS, click here to check out October 2008 issue of Nature Biotechnology.

Read more...

Seminar on Plant genomics

Title: Recent advances in plant genomics research and analysis
Presenter: Prof. Chris Lamb, Director of John Innes Centre, UK &
Dr. Jane Rogers, Director of The Genome Analysis Centre, UK.
Date: 26 Mac 2009 (Thurs)
Time: 1.30-4.15 pm
Venue: Sky view 7, Level 29, The Gardens, Mid valley, KL.
Organizer: MGRC

By invitation. If you have not heard about this seminar, either you haven't check your emails or you're not in MGRC mailing list.

Read more...

Health & peace talk by Nobel Laureate winner

Title: Biomedical science, world health and world peace
Presenter: Prof Howard Robert Horvitz,
Nobel prize winner of Medicine in 2002
Date: 16 Mac 2009 (Mon)
Time: 2 pm
Venue: Bilik Senat, Canselori, UKM.

Open to everyone.

Read more...

Career in Biotechnology 13 Mac 09

Title: Career in Biotechnology
Orgnizer: Malaysia Biotechnology Sdn. Bhd.
Date: 13 Mac 2009 (Fri)
Time: 3-5pm
Venue: G129BB, Bangunan Biologi, FST, UKM.

Open to all final year students and staff.

Read more...

SOLiD Bioinformatics workshop, 10 Mac 09

Today, Analisa Resources and Applied Biosystems organized a great seminar and workshop as an introduction to SOLiD data analysis in Malaysia Genome Institute (MGI).

I apologize because I didn't post this up earlier. I only received the agenda last night. I'm glad I went. I hope I have time to write a nice post on this next week.

Read more...

Inbiosis seminar 11 Mac 09

Title: The use of microarray in investigating asthma
Presenter: Prof. Madya Dr. Roslan Harun, UMBI.
Date: 11 Mac 2009 (Wed)
Time: 4-5pm
Venue: Bilik Seminar, Inbiosis, UKM.

Open seminar. For more information, please email inbiosis.seminar.series@gmail.com

Read more...

Jungle trekking in Pulau Redang

The weather is perfect. The sun is shining brightly despite the predicted rainstorm The blue ocean is inviting. The sunlight is reflected on the surface as the sea wrinkles and crawls to the beach. That was my first impression when I arrived at Redang island last wednesday.

I’m sure everyone is familiar with Redang. It is an island in Terengganu famous for its beautiful beaches and rich marine life. Not many people know that actually Pulau Redang is also rich in both flora and fauna. Among the species that can be found are macaque monkeys, mousedeer, monitor lizard, snake, geckos, over 50 species of birds, 84 species of butterflies etc. If you are tired of snorkeling, you might consider spending 2 hours for jungle trekking.

The jungle trekking trail starts from the backyard of Coral Redang Resort and it leads to Berjaya resort. All you need to do is follow the orange TNB (Tenaga National Berhad) pipeline. Also, look out for ropes or tree trunks that are painted in red.

On the second day of my trip, we headed out after lunch. We were lucky because the trail is quite dry. We found a snake skeleton after a mere 5 min walk. As we proceed cautiously, I saw a Sang Kancil (mousedeer) running away from me after hearing my loud footsteps. The track gets more exciting as we crossed several rivers and climb up the hills. It took us awhile to figure out where is the trail when it’s impossible to walk next the orange pipe.

What amazes me the most is to find a few Monkey cups plants (Nepenthes sp. or pitcher plant). It got its name because monkeys are often spotted drinking water from the plant. These plants growing out from the vines can run several meters. To the Chinese, Monkey cups are signs of prosperity. The local Chinese saying is 朱笼进水十八十八 .When it’s pronounced in Cantonese, it means that if you collect 18 monkey cups, you’ll be rich when the water enters them (This is my translation version). Usually the first thing I'll do is to peek into the cup for any trapped insect and then pour the water out. Old habit hard to die. Monkey cups are rare these days SO PLEASE DO NOT DAMAGE the plant or remove the cup from the leaf!!!

When walking through the forest, always be alert of any surrounding sound. Try to look up the trees when you heard birds chirping. This is how I spotted two exotic bird species with long tails. Due to my "over-sensitiveness", I was surprised several times at the loud noises made by some tiny lizards.

After trekking for 50 mins, we stopped at the sight of monkeys fighting on the trees. We were so close to our destination because we can hear the sounds of waves crashing onto the shore! Yet, we have no choice but to head back to the resort for our 2.30 pm snorkeling trip.

I would say that this trail is a bit challenging because there’s a place that is very steep. You need to hold on to the ropes which had been tied to the trees to get down the hill. I have done even steeper trekking in Hulu Langat last year at NIGHT! If I were to rank this trail, I would give it a 7 in terms of challenge and 9 out of 10 in terms of biodiversity. One of the best adventures I had because there’s so much to see.

Note:
Unfortunately, I wasn’t able to visit the turtle sanctuary in Redang because according to the resort staff, that place can only be reached by boat. The turtle volunteer program is offered every year. For more information, visit www.umt.edu.my/turtle.

Read more...

On Vacation

This blog will be inactive for a few days because I'll be on vacation. Finally!!!

I’m going to Redang! I was lucky to find really cheap flight tickets to KT and got an early bird 3D2N snorkeling package promotion. I have been waiting for my next snorkeling trip since I returned from Sabah for more than a year. Getting tan is the only thing I don’t look forward in this trip. I also hope to write a nice post on turtle conservation in Pulau Redang that I have heard so much recently.

Read more...