Here comes my Phd project!

It is 4.40pm. I am waiting for my "mummy" to spare sometimes on my current project. I am going to show her my web design and the interfaces which I have put a lot of effort on it last three months.

At last, I am asked to enter her room to demo my project. I have planned well and be well prepared. The demostration lasts only 5 minutes. I know I have make enough materials to surprise her.

She is going to take leave next week. I take the chance to tell her my project`s problem. It is mainly the hardware problem. Having enough of programming skills but still the PC in pasca room are far to be consider as good workstation for my "presentation". I ask Dr to setup cluster computers. She have agreed with me.

In the same time, she also finally show me my long-waits phd project. It is actually a huge project in INBIOSIS. Involves almosts every lecturers in BsBt, FST. The project is known as Arus Perdana. Something involves metabolics study in omics level. Yup, it is known as metabolomics.

The projects involve wet labs in MGI, whereas dry lab in INBIOSIS. As I skim on the proposals, it takes about 10 years to finish the project if everythings work well as in the proposal. The computational part (dry lab) will take almosts 5-6 years. My phd project will be the computational parts. Building pipelines, databases, integrated systems. I have been shocked with the objectives to be achieved.

Seems like I will not be free for the next few years. God, do bless me have a fluent progress. I would certainly be very appreciated on that.

Roll out! KK. I can do it!

Sick for one week...

While my worklife filled with unfinished tasks... I was caught sicked in this week. Starting from Monday, I used to go to INBIOSIS as usual but that day there is an air-con system breakdown. Like they said.. we have a free sauna at INBIOSIS.. I can`t believe it that I have stayed in the lab till 1pm... honestly, I wish I can stay there till 5pm but.. that day happens to be not my "fit-condition" day...

At Monday night.. the fever is striking to my head causing headacne. I felt weak and yet start to cough.. Terrible fever.

With fluctuating fever heat, I stay on my bed for the rest of the days.. With some rests, I managed to have some short period of "good" condition but it just can`t stay long.

Finally, I have went to clinic to meet the doctor. Nice clinic and nice doctor. She gave me some antibiotics, pills for fever and drug for coughing. With the aids of medicine.. I feel well now. However, really dislike the effects of taking drugs. It left up some disgusting feel. Nevertheless, I am still getting well now.

With the week of fallen sick, next week will undoubtly be my "busy" week. God, please do bless me.

Third week as RA in INBIOSIS

Starting from 11th of June, I have finally acquired my bachelor degree from Universiti Kebangsaan Malaysia (UKM)!

When I was about to click on the show result link in SMPWEB, UKM`s student academic management site, I am very nervous...

"what I am going to get in my last semester in UKM?"

That`s question keeps on emerging in my mind. For the first time, I do dream that I may get a 4.00 in the last semester. How good it is if it is the truth.. haha... My daydreaming habits had became seriously at that moment.. I have already been told that one of my major is going to be A-... cell molecular biology... how poor it is.

I thought I may get an A for sign language but it appears to be another A- too... So 4 subjects... 2 A- and 2 A, that`s my final result. Not too good and not too bad at all, wasn`t it?

Thats drew up the beautiful fullstop in my undergraduate life in UKM. After my painful experience in second year, everythings seems going back to its original track pace now. Glad to have that improvements.

That was my second weeks to work as research assistant in INBIOSIS while the results is released. I have been assigned a challenging task from my faithful Dr Zeti. To prepare the final paper for my EST pipeline! This is going to be my second research paper soon.

However, the problem is, the pipeline is very competitive. Just 2 months, there have been great improvements in the field. New algorithms and programs are popped out like the mushrooms after the raining. I have to refine my pipeline, look for new possible developments.

This week is my third week to work in INBIOSIS. Dr Zeti have assigned me another task.. That is to be the server admin in INBIOSIS. I have finally have my own working office or perhaps better to say it is a lab. Haha...cool!

The room is known as instrumental room, which hosts three servers in INBIOSIS. I am going to setup the Windows-platform one, and keep an eyes on the other Mac-based server.

In order to keep the server cool, perhaps due to their 24/7 working hours, the air-cond is set to 10 degree... very cool man! And yes, my lab is in air-cond... the coolest one..haha!

The servers in the instrumental room are all producing annoying noise while running... I think I need to bring and headset while working in there later and one more thing is my jacket off course!

Having a new room to work and two PC to stand beside me... that is nothing better than that...

New life at INBIOSIS

I have started to work as a lab assistant at INBIOSIS last week. The feelings is like going to industrial training. I am still being allocated at the post-graduate room that filled will windows PC.. haha... there are being arranged differently now...

Right of the first day, Dr have assigned me a two-week project. That is to finish my pipeline manuscript. The pipeline is in infant phase which has many to be developed. My little son is very naugthy..haha.

Spending some days to look for latest literatures. The field is really full with competitions. Only two months time, already pop up will new pipelines, better programs and better interfaces... haiz...

To achieve the novelty, have a lot to do.. perhaps need more creativity.. and some sparks of inspirations. Dunno can make it or not.. gonna day-dream a lot.. hehe.

Still leave with one week time, gonna run the deadline... T-T Days with lots of work... when will it be ended? (Sometimes, I rather want more works than playing around with nothing to do, how complicated I am haha...)

PHD...

I have received two options from my supervisor about my PHD study two days ago. She have offered me another choice which is New Zealand (her research collabolations in future). Dr. Alexei Drummond.. is the collabolator there.

I was asked to make a choice. Dr Alexei Drummond is specialized on phylogenetic analysis. He have developed a lot of Bayesian Phylogenetic Analysis software. The most recent project involved developing geographical phylogenetic analysis system. It is very interesting on the topics (I myself like phylo before stepped into EST...)

However, now I have been quite an expert in EST now... Not really sure wanna give up further research on EST or not and to pursuit another totally new area to me... It is really hard to make the choice.. hai...why on earth so many options...

Australia or New Zealand? I have to make decision before 22 of May. In order to apply for scholarship, I need to prepare a proposal on my PHD research.. It is going to be EST (genomics related, perhaps transcriptomics is more accurate) or phylogenetics (with Bayesian analysis... and geological knowledge). No matter what I choose, it is going to be a new challenge to me!

The day after thesis presentation...

At last, I have presented my undergraduate final year project! After correcting what I suppose to correct, reprint it, and then get my supervisor`s approval to bind my thesis, I have finally put my order at xerox shop near KTM (used to called 5G).

The time I went back my rented home, I was very happy and tired. I have a kind of weird feeling, feeling happy that my thesis have finally been completed with "Excellent job!" from my supervisor; but in the same time... I guess, I am going to say good bye to some of my friends in UKM...

I know that this day will come, there are always people that came across in our life some times, and they usually will leave on one day too. This is something that can`t be avoided, perhaps in everyone`s daily life. 

I really will miss all my friends in UKM soon. However, I do wish them to have a good fortune and get a good job soon. I will move on too, applying scholarships, get a phd degree.

I hope that one day I can established an academy of Bioinformatics in Malaysia. I love to train young bioinformaticians and looking them to work as a team in biological research. 

I am going to start my RA at INBIOSIS soon. Hope to get more knowledge and more reliable skills in research before I go oversea to compete with others.

The potential of cloud computing

I have been PHP programmers since 2007, however, it was just 2 years later that the computing technology is evolving again. This time is what they called cloud computing. 

I was told by Sun Microsystems that they are now contributing cloud computing technology to the users. What is cloud computing? It is a new term appearings in this year. I do read about it in the IT sessions of newspaper a few months ago. 

There was something came up in my mind that "is it okay to use this new technology in bioinformatics?" That ideas sounds interesting and I started to look for literatures. It is surprisingly yes, there are people start noticing the potential of cloud computing in the bioinformatics field. What is amazing me is that they said if PHP and MySQL is the famous web scripting language and database in 2008, then the next round of it will be the technology in cloud computing!

Cloud computing, the concept is to make all the services done in desktop or laptop to go "online", that means, we all can use the softwares as web services without installing it into our computer. What we need is just input and output to upload and download. This idea is good when it comes to biologist that lacks of computer sciences knowledges (especially linux based tools in bioinformatics). 

Cloud computing surely will be a good direction to be explored in bioinformatics, I have proudly inserted it into my list of studying during free time. It makes me excited and scare when the list is keep on increased in length but the free time is limited. There is much more to learn in my field, I guess.

Today, I have received an email from MGRC, Malaysian Genome Research Center, that they have chinese version of their website! How nice it is. This shows the importance of chinese in bioinformatics, which has much developments in China. As a chinese, I am very happy to know the news. It is an advantage to learn chinese since some of the research in China are novel and advanced. This will soon increase the market of MGRC in China perhaps. 

Learning is a long life task, no one should stop from learning each day. However, the road to be a master is far more than just learning plainly... because what we learn is previous exprience of our ancestors, we should be improved and get the ability to create new knowledge, that is what makes a difference to an expert and a master. 

匠与宗师的区别就是，一个在用，一个却去创！

Cooking and programming...

When I was in the second year in UKM, I learnt how to cook from my mom. That was an unexpected consequence that it help me a lot to build up my programming sense in my future study.

I was taking web programming that time, it is really headache when deal with javascript and css. Those are scripting languages that I used to learn in my early age at 15. But I do like HTML, and I am really the type of programmers that don`t have talent on designing, that is why CSS is really hard to me.

However, when I was taught on how to cook, chinese dishes, I somehow found the connection between programming and cooking... FTSM courses suddenly becomes fun to me and I do, like programming very much since then.

When cooking, there are various of things to consider.. I have to prepare the ingredients from major materials to supplements. I have to washed them carefully, cut them in pieces sometimes , it just like defining the valuables in C++, have to setup each datatype, what is integer, what is character and strings... haha... the ingredients are all programs inputs!

The steps in cooking, some have to fry, steam, rinse.. each of them requires different degree of fire level.. it is analogous to programming when we have selection, loop, and condition... IF the meat is yellow enough, THEN off fire... haha... I used to create my own programming codes during cooking...It is really fun!

Let`s go back to web programming, I don`t have the talent to design... that is what I know since I was young... webpage layouts is really not the place for me to perform well, but after I learn how to cook, I have to arrange the dishes, decorate it a bit... that makes me pay attention to web layout. It makes me feel that I do can`t escape from preparing good layout for my programs output... haha... imagine dishes which is not in nice shape, who would dare to eat it even it was told it is delicious... That took me a week time in my semester break to study CSS... It is worth to do it, cause it really help a lot in beautify my webpages... hehe.

Cooking requires me to tidy the utensils and supplements nicely. I have to know where the salts and sugars is, so that during the cooking, can have it easily. It gives me the chance to practice database knowledge here... I relates each materials and try to query it like SELECT meat, vege, tomato, sugar, pepper FROM kitchen, cupboard, recipe WHERE cupboard.supply_id=recipe.id... practicing SQL combination in kitchen...

Speaking about cooking rice and porridge, it is the matter of fuzziness in dealing with water and paddy...hehe, practicing FUZZY for AI during rice cooking... That doesn`t count for the control of fire during cooking too...

Integrating study with life is one of my secret in my study philosophy... Everyone can do that.. It is the CORRECT ways to applied our knowledge...

If you creative enough, you can makes all the skills you learnt in bioinformatics being applied in any works or task in future.

My own comments after 3 years in UKM,
Don`t waste your money and time in university, start figure it out your own way to applied all those knowledge. I think that will be more meaningful that chasing pointers...

Life to 30 - Intro

Life 2 30...

I am going to finish my undergraduate study soon... perhaps another 140 days or 3.5 months.

Life in university was really tough, but challenging. I am glad I have acheived something that I hope for before I leave the U.

3 years was not a very long time, but do have many things happened that make me change a lot. I had learnt from the past and from there, I developed my own strength, my own philosophy towards life. Right in front of me, is my new journey. Another 3 years or maybe longer.

This time is even far away than my loving home. I am going to take much more tougher challenges, something that I am not sure whether I have prepared for it or not. Somehow I know that life is not going to stop for me, I have to move on.

I open up this blog to keep tracks of my journey towards the age of 30 with the goal to be the best bioinformatician in Malaysia!