Bioinformatics for Biologist: Installing NGS software

I remember I have difficulty install Velvet, the first Next Generation Sequencing software I use. As a biologist, I just don't understand how to install despite reading the manual many times. Once I did, NGS software installation becomes simple. Occasionally I run into problems. Maq and MapView are among the hardest softwares to install. Here, I'm gonna share how to install a NGS software.

Installation
The NGS softwares are compressed in a tar.gz file. Once downloaded, right click and select "Extract here". A folder with the same name will appear. It's your choice to install in which directory. Preferably in a hard disk (not Desktop or Documents) as the file generated will take a lot of space.

To install, ALWAYS read the manual or README.txt for instructions. Instructions differ for each software. Some softwares like Samtools are ready to run once unzipped. The two basic commands to install are:
> make
> make install

Here's an example, I just downloaded BWA 0.5.5 from http://sourceforge.net/projects/bio-bwa/files/. After unzipping it, I found no instruction to install. I thought it's ready to use. But command "./bwa" doesn't work. So I tried "make install" and "make". Only the latter works. During installation, there will be a long list in the Terminal to check if the required files/libraries/systems are present.

Once the installation completed, I type "./bwa". A help file with a list of options appeared. In bwa-0.5.5 folder, you will notice many files are added during installation. Mission accomplished.


Troubleshooting
When you fail to install it, the Terminal will show "ERROR" or "Stop". If you wanna know what went wrong, you need to check the lines that Terminal produces during Installation. Maybe you didn't install a library or some GNU environment required. Once missing components are identified, go to System > Administration > Synaptic package manager to install them. Try installation again.

Tutorial
Let's try installing maq-0.7.1. I have problem installing this version eventhough I was certain I have all the components installed. I even tried to install an older version 0.6.8 but it didn't work. Took me awhile to figure out what's missing.

For installation instruction, read http://maq.sourceforge.net/maq-man.shtml#install. To download, http://sourceforge.net/projects/maq/files/maq/

Why don't you try it on your own first. Just download the zip file, unpack it and simply type on Terminal:

./configure; make; make install

Alternatively, you can also type 3 separate commands:
>./configure
>make
>make install

If you manage to install it, congratulations! If you don't, welcome to the club!

OK. Let's cut the chase and tell you what I did to fix the problem. I realized a library known as "zlib1g-dev" is missing. After installing that library, I type:
>./configure
>make
>sudo make install
Then, type in administrator password and Wala!

Since I already install the library needed, I can't show you an example of failed installation. Oh this is the worst tutorial ever!

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Bioinformatics for biologist: Using terminal

One of the first things in Bioinformatics is learning how to use Operating Systems (OS) other than Windows such as Linux and Mac. I'm currently dual-boot 64-bit Ubuntu with Windows Vista. What's the different between 64-bit and normal 32-bit? 64-bit OS enable more than 4 GB RAM usage. But don't bother buying 64-bit Windows because most NGS tools are built and tested on 64 bit Linux OS. My advice is to get a free 64-bit Linux distro which is suitable for you.

And, most tools run on command line instead of Graphic User Interface(GUI). In fact, many bioinformatians think it's a stupid idea to create a program in GUI. Who needs GUI? Biologist does.

The command line is run using a shell. The shell in Ubuntu is called Terminal. To open Terminal, click on Applications menu -> Accessories -> Terminal.

Let's look at some of the basic operations I use daily:

cd
To change directory. Directory can be refered to as Folder in Windows term.
cd ..
Back to previous directory
cd /
Back to root directory

ls
list the file/directory in the current directory.
ls *.pl
List all the file/directory ending with ".pl". For example, fastq2fasta.pl will be listed.
ls fastq*
List all the file/directory starting with "fastq".
It's easy to find a file if you cannot remember part of the file name.


rm
Remove a file or directory

wc -l filename
Count the number of lines in a file. Useful to find out the number of sequences in a FASTA file. # sequences = # lines divided by 2

split -l 20000 filename
Create smaller files consisting of 20000 lines each. Type "split --help" for more split options.

more filename
Read the content of the file from beginning. This is very useful when the file size is very big (>100MB). Opening it using a text editor will crash the system. Press ENTER to read more lines.

top
Display information about system, running processes and RAM usage. To exit, press 'q'.

sudo
Root user or administrator. Any command starting with "sudo" requires administrator password.
sudo rm -rf ~/.local/share/Trash/files/*
Administrative privilege used to empty trash.

When typing a long command on terminal, you would prefer to paste that command there. Note that Terminal is different. To copy something from Terminal, hightlight and press shift+ctrl+c. To paste onto Terminal, press shift+ctrl+v. Alternatively, you can right-click your mouse and choose the copy/paste option.

When a command or application finish running, you will see the directory address with "~$" sign again. To stop any running application, press shift+ctrl+z.

Find out more on https://help.ubuntu.com/community/UsingTheTerminal

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It's 2010! I'm back!

Sunset at Tian'anmen

It's been two weeks since I came back. Haven't check my blog until now. I'm sure somebody will be curious where I went for the past four months. I was traveling. I spent almost three months doing an attachment in China. Mainly bioinformatics analysis.

Hmmm... what should I write in the first post of 2010?! A notification that I'm back ofcourse. :p Considering how busy I am lately, I don't think I have much time to update my blog regularly. It's a pity. Oh well, I guess I will just make a quick post everytime I think of something.

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It's vacation time!

Yeah! The long-awaited vacation is just around the corner. Then, I'll leave Malaysia to do an attachment. See you next year! :p

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Some recent thoughts (August 09)

Busy... seems like the only word I always use to describe my life. lol... I think people are tired of hearing that word from me.

At the end of August, I attended the MSMBB post-conference symposium. After looking at the programme and speaker list, there's no way I can miss this. I was right. Not only did I gain so much knowledge, it's a nice break from my busy life for a couple of days. It gives me new ideas and directions on my work. When I interact with other researchers, I feel very excited about the new things i can do. Enthuasiasm is contagious. I took the advice of the organizer to go home, think about what I wanna do next and write it down. Suddenly, I feel that those few days are so well-spent.

So next time you feel like you can't breathe or what my housemate call "living everyday like a photocopy machine", just take a break to attend a seminar or conference. Go home, think, and write a note.

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GRA vacancy

GRA vacancies at INBIOSIS, UKM
BSc (Honors) in biochemistry, food science or analytic chemistry & >CGPA 3.0 required.Deadline is 8 Sept 09. Please email CV to Dr. Syarul Nataqain nataqain@ukm.my or Dr. Maizom maizom@ukm.my


GRA vacancy at UPM

• Background in biology/genetics/biotechnology/biochemistry/forestry
• CGPA> 3.5
• will pursue a MSc/PhD
• preferably with own transport
• project involves gene cloning and characteristics

Please email Dr. Rozi rozimohd@putra.upm.edu.my with GRA subject heading.

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A lecture on AH1NI

This is not a post that is related to my research but I will share what I can understand clearly from the talk. It begins with an introductory speech on "genetic variation key to survivor" by MGRC founder, Dr. Robert Hercus. It’s interesting as I was not aware of the fact that viruses such as HIV has millions of variants. There are more than 4 types of dengue viruses. A virus genome is about 10kb, so it’s fairly easy to sequence thousands of variants per day. Before getting to the eminent speaker lecture by Dr. John McCauley from National Institute for Medical Research (UK), Prof. Ramlan from UPM gave us a talk on animal influenza and some insights into virology.

What are influenza virus?
According to Wikipedia, influenza viruses are RNA viruses of the family Orthomyxoviridae that cause flu in birds and mammals. The viruses can be classified according to species ABC, strains and genotypes which can be divided into claudes. The surface proteins, HA and NA subunits play important roles in infection. Therefore, most viruses are named based on these proteins: H5N1, H1N1 etc. It's important to note that the AH1N1 virus contains RNA genome instead of DNA. The genome is divided into 8 segments. The reassortment of genes is a major concern.

So is H1N1 new?

The answer is NO. The Spanish flu 1918 originated from a subtype of H1N1. The common types of swine flu found in pigs are H1N1, H1N2 and H3n2. There are about 1.5 million pigs in Malaysia. Based on a survey carried out by Prof. Ramlan and his team, classic influenza virus are detected in some of the 800 samples tested. The common detection method used is RT-Elisa-PCR while researchers all over the world use Real-time PCR to confirm the presence of AH1N1 virus accurately.

"A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before human emergence." -Smith et al. 2009, Nature.

According to this paper published in Nature, the new virus is the combination of several other influenza viruses. Based on the phylogeny study of the proteins, it's closely related to Hong Kong H1N1 virus. It's interesting to see that bioinformatics play such a big role in this discovery.

Why did the new virus go undetected for years?

Dr. John McCauley explained that this is due to the lack of swine flu prevention measures taken by all the countries. The flu symptoms are mild i.e. lose weight and abortion.

When will the vaccine be available?
Autumn. Exact date? Unknown.

Why is the vacinne taking so long?

It definitely is taking faster than any other vaccine production. Bear in mind that it's a long process. The right virus strains must be first identified. The virus is incubated in the egg. Optimization is crucial to ensure large-scale production. Clinical trial and quality control must be carried out. Lastly, it involves licensing and other legal actions to make it available in the market.

What lessons can we learn?
Governments have to invest heavily on influenza viruses R&D. More effective prevention measures must be taken by all the countries on the next outbreak. Faster drugs and vaccines development. It's a matter of time before the virus become resistant to Tamilflu. Nobody can tell where all this is all going. Everyone is waiting to see what happens next.

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Short lecture on basic in Bioinformatics

I'm attending a MSMBB post-conference workshop right now. Prof. Shoba just gave a brief lecture on basics in Bioinformatics. I'll just post a quick note with my own opinion added.

Bioinformatics is the application of computational methods in system biology. Bioinformatician deals mainly with protein and DNA sequences. The sequences are treated as linear sequences. It means that the backbone of the DNA or protein is ignored and only residues are important. They also have to deal with 3D structures using specific software. Bioinformatics helps biologist to understand a biological process and shorten the time of lab work. Therefore, they also spend a lot of time communicating with biologists and reading about the subject.

Let's take a look at the history of bioinformatics that is focused mainly on DNA sequences. In 1980, bioinformatics projects were initiated to look at protein structures. When Sanger sequencing was introduced, more works are carried out in analyzing DNA sequences. In 1990, the Human Genome Sequencing project was announced and was completed in 2000. Everyone was very excited about the sequences. That was when what people call the "false dawn of bioinformatics era". The real dawn of bioinformatics came when the Next Generation Sequencing was introduced in 2005. Subsequently to be replaced by 3rd Generation Sequencing. Expertise in these fields are highly sought after in the market.

Careers in Bioinformatics

Genomics:

• Genome sequencing
• Comparative genomics
• annotation and mapping
• gene discovery

Pharmacogenomics:

• SNPs
  
• therapeutic target recognition
  
• pathway effects
  
• drug and expression effects

Proteomics:

• proteomics
• protein profiling
• alternate splice
• structural genomics
• drug and vaccine design

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Useful ways to prevent email hacking

Recently, I received several emails from a few colleagues that has similar content. First, they said they were trapped in a hotel room without any reception (except internet access). They were asking for my help to get them out of there. For example, bank in USD20,000 into this account before this particular time. I swear they came to work on that day. So, there's no other explanation other than their email accounts are hacked!

This is a serious problem. This cannot happen to me! So, how can I prevent my account from being hacked? First of all, use a difficult password with capital letters and numbers. Change the password regularly. Do not leave any important emails in your inbox for the fear of losing them.

Sounds easy but the truth is these tips will never work! Hackers can easily download a free software online and get it running at no time. To know how to prevent, we must first know how email account hacking software works. The key is to think like a hacker! :p

Here's some useful tips I found:

• Do not open any email if you don't know the sender.
• Never reply any email that ask for your email or password. Can't believe people still fall for this!
• Another trick hackers used is to create an identical webpage similar to your login page. Once you type in your account and password, your email account is gone.
• Never download any files from unknown sender. You might install the hacking software into your computer. It can run automatically like a trojan horse and send your information to the hacker. Your anti-virus might not be able to detect it.
  
• Safeguard your computer. Never give anyone a chance to install the hacking software in your computer.

For safety reasons, I will delete any blog comments containing email address.

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International Conference on Natural Resources and Environmental

International conference on Natural Resources and Environmental Management and Environmental Safety and Health 2009

Theme: Understanding the causes and impacts of climate change
Date: 24-26 November 2009
Venue: Hilton Hotel, Kuching, Malaysia
registration fees: RM300 (Student)

KUCHINGGGG!!!!!

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