Bioinformatics for Biologist: More efficient ways to run all-against-all blast

All-against-all blast is used when we want to search the sequences against themselves using blast. It is useful to look for paralogous genes and alternative splicing isoforms within a dataset. Basically, it involves two simple steps: 1) Create the database; 2) Blast the sequence file to its own database. You can specify which blast and algorithm to use. It is similar to the normal blast except it uses the database created from its sequence file. An example of the commands are as follow:

./makeblastdb -in file1.fa -dbtype nucl -out database1

./blastn -task megablast -db file1 -query file1.fa -out results1.txt -evalue 1E-10 -outfmt 6

However, the process takes a long time and produce a large output file because it will report huge amount of alignments of the same sequence against itself  ("Seq1 Seq1"). What we are really interested in are the alignments from "Seq1 Seq2" or "Seq1 Seq3" etc .When I run blastn -blastn on a 20MB file, I estimated that it will take 16 hours and produce several GB of output. When I realized the long running time required and large output file produced, I immediately stopped the analysis. When I googled this problem, I found very few resources available, namely one discussion on Biostar, one Python script and an old software NBLAST which was published in 2002. 

Here is the step-by-step guide on how I do all-against-all blast more efficiently:

1) Reduce the time by spliting the sequence file into several files and run blast simultaneously on these files (as suggested in Biostar discussion). 

Using AWK, I can split the files by first splitting the file using ">" and specifying the record numbers for each smaller files. This is an example for a file which contains 66902 sequences. This script removes the first record which is empty. It gives 16724 sequences to the first three files and 16730 sequences to the last file. 

awk 'BEGIN{RS=">"}NR>=1&&NR<=16725{print ">"$0}' file1.fa > file1.fa1

awk 'BEGIN{RS=">"}NR>=16726&&NR<=33449{print ">"$0}' file1.fa > file1.fa2

awk 'BEGIN{RS=">"}NR>=33450&&NR<=50173{print ">"$0}' file1.fa  > file1.fa3

awk 'BEGIN{RS=">"}NR>=50174{print ">"$0}' file.fa > file1.fa4

2) To remove the alignments resulted from the same sequences. Instead of specifying the output file in the blast command, I pipe the output to AWK which will remove the alignments that has the same subject and query sequence. I also performed additional filtering for alignments with at least 40% identity and at least 300 bp of alignment length . 

blastn -task megablast -db database1 -query file1.fa1 -evalue 1E-10 -outfmt 6 | awk '$1!=$2 && $3>=40 && $4>=300' > file1_1.blast

Note: If you're dealing with sequences which contain several alternative spliceforms, you might consider using the following command. This will remove the alignments between contig001.1 and contig001.2.

blastn -task megablast -db database1 -query file1.fa1 -evalue 1E-10 -outfmt 6 | awk '{split($1,a,"."); split($1,b,"."); if (a[1]!=b[1] && $3>=40 && $4>=300) print }' > file1_1.blast

3) Lastly, we need to remove the redundant alignment from any two sequences. For seq1 and seq2, you will find two highly identical alignments, namely "Seq1 Seq2" and "Seq2 Seq1". However, these two alignments can differ slightly in alignment length etc. Therefore, the best way to remove them is by using total score (column 12).

awk '{c=$1"\t"$2"\t"$12 ; b= $2"\t"$1"\t"$12; if (c in a  == 0 && b in a == 0) a[$1"\t"$2"\t"$12]=$0}END{for (i in a) print a[i]}' file1_1.blast > file1_1fil.blast

Related post:

Bioinformatics for Biologist: Installing standalone BLAST+ on linux

Read more...

Applying 80/20 rule in bioinformatics analysis

I have always been a firm believer in quality before speed. Ever since I read about the 80/20 rule last month, I start questioning how productive are the things I do. It allows me to reflect on my strengths and weaknesses. Just two weeks ago, I recorded my personal fastest time to complete an analysis from scatch. It took me less than a day to assemble some 454 sequences I downloaded from NCBI SRA! I spent half a day for installation and half an hour to assemble (well, it was a small dataset). I thought I would need more than a week to trim, filter reads, install, try different software and try different parameters etc. Instead, I settled for "good enough" assembly and save the time for more important tasks. 

What is 80/20 rule? It is also known as Pareto principle which is developed by an Italian economist, Vilfredo Pareto. In 1906, he observed that 80% of the wealth was owned by 20% of the population. This concept has been widely applied in business. Although the real ratio always derive from 80/20, the rule generally implies that most results come from a small amount of efforts while a large proportion of efforts give very little impact or result. By investing our efforts on the 20% of work that is really important and reducing efforts on 80% work that is least important, we can increase our output tremendously. 

Identifying 80/20 rule in bioinformatics analysis. First, I need to breakdown my workflow into steps and identify which area is consuming more time and how to improve my efficiency. The flowchart below shows my typical bioinformatics analysis which involves four basic steps :1) Identification of appropriate bioinformatics tools; 2) Reading manuals and publications; 3) Installation; 4) Running analysis.

Running analysis is the 20% work that will give me 80% results. The most exhausting stage is choosing the appropriate tools, reading publications and manual, and installation. So naturally, I would want to reduce the time I spent in these areas. But how?

• Do I really need to install the software locally? Is any web-server available? Are there any  written scripts by good samaritians available online? Big dataset?

• Choosing the appropriate software. Mostly I have several software options. I will start with the most popular, well-supported and well documented software. Is the software up-to-date and the last release date is recent? If no, then there is a good chance that I will not be able to install it in my system.  

• Reading manual. Some manuals can be 200 pages long while some can be as short as a README text file. By skimming through the whole manual and reading only what I need, I can save a lot of time. I always read the part on introduction, installation and the analysis I need. 

• Installation. I always make sure I installed the required packages and dependancies before installing the software. Some software developers will not tell you this in the manual, and therefore, be sure to google it online.

• The software may not be working properly due to various reasons such as incomplete installation and wrong input files. To identify the problems, I usually test run a small dataset. My latest practise is to save the print screens into a log file to look for errors.

• It's time to call for help if the step above still can't solve the problem. The fastest way is of course by goggling the problem online. I realized that I can find a solution faster if I know the specific problem, error message and right syntax to look for. Posting at a forum or writing to the developer is the last resort as it may take a few days before I get a reply. 

• Do something productive while waiting for the analysis to complete. I'm drafting this blog as I'm running Genscan locally. Estimating the running time is very helpful in managing my time but I often don't know how long it will take. I have a little Unix trick that will play a sound when the command finished running. In that way, I get notified when the analysis complete. Whatever you plan to do during the waiting time, be prepared to be interrupted once the analysis has completed.

Free feel to post any suggestion in the comment box.

Read more...

Ten botanical gardens in Europe

Recently I spent six weeks in Europe as my graduation vacation. It was a great time to be in Europe because it was spring although it arrived late this year. It's interesting to know that there is almost one botanical garden in every major city. When the weather is sunny and warm, locals and tourists flock to parks and gardens to have a picnic and relax. I enjoy going to these botanical gardens because I like to learn more about plants specially temperate plants. A visit to the botanical garden always make me feel inspired, connected to the nature and started dreaming having my own garden. Unfortunately, many of these botanical gardens require an entrance fee. I only visited a few due to time and cost constraint.

According to Wikipedia,  botanical garden is a well-tended area displaying a wide range of plants labelled with their botanical names. Botanical garden first started as a collection of spices, plants of medicinal and economic importance. There were many small garden in monasteries to provide food for monks. It was in one of these gardens that the fundamentals of genetics, the Mendel's law was created. These gardens continued to be maintained over the years and the few left were turned into the botanical gardens of universities. A detailed history botanical garden can be found in this link. Besides botany, botanical gardens play a big role in plant conservation, education, research and general public interest.

My online search for a comprehensive list of botanical gardens in Europe did not yield expected results. There is a list of botanical gardens in European Botanical Garden Consortium but it is not complete. Most lists and reviews are posted by traveling websites (see the following). Therefore, these articles are written according to the interest of tourists and can limited by the writer's experience.

• Garden and Park guide from European Tourist Guide (The most comprehensive list I found)
• Favourite European Gardens from About.com (8 botanical gardens listed)
• Botanical gardens in Europe from Lonely Planet Guide (Just two in the list?! You're kidding!) 
• 10 botanical gardens you should visit from Audley Travel (Around the world)

So where are the list and reviews for plant enthusiasts like me? I guess I have to come up with my own list (sorted according to the order of my visit). Scroll down to see reviews and photos.

1. Kew Garden (London, UK)
2. Jardin Des Plantes (Paris, France)
3. Keukenhof garden (The Netherlands)
4. Botanical garden, University of Utrecht (Utrecht, The Netherlands)
5. Hortus Botanicus, University of Leiden (Leiden, The Netherlands)
6. Botanical garden, University of Potsdam (near Berlin, Germany)
7. Palm Garden of Hofburg palace (Vienna, Austria)
8. Schonbrunn palace (Vienna, Austria)
9. Botanical Garden, University of Vienna (Vienna, Austria)
10. Garden of Pitti Palace (Florence, Italy)

1. Kew Garden
Location: London, England
Admission: GBP 16
Review:

Famous for the world's oldest and largest herbarium. One can easily spend the whole day here exploring the conservatory, green houses and many other attractions in the garden. This place is more than just flowers and trees. Birds, lake, pond, arts, English countryside, river, plant market, you name it! When I was there in mid April, the cherry blossom, glory of snow, magnolia, daffodil and narcissus are in full bloom. I was delighted to see a few Eucalpytus and redwoods such as Sequoia giganteum. The weather was warm and sunny in the morning before turning to gloomy and cold weather in the late afternoon. The admission fee is pricey considering London is famous for free entrance into museums. Lucky for me, a friend doing a PhD there took me in for free! 

 Clockwise from top left: Main entrance and souvenir shop, Princess of Wales Conservatory, research building and herbarium.

 Clockwise from top left: Pink cherry blossom, blue flowers known as Glory Of Snow, an old and lazy tree which grows sideway, spring flowers in the greenhouse, Bonsai apple tree.

Clockwise from top left: Chinese pagoda, English cottage, tree platform, Japanese garden. 

2. Jardin Des Plantes
Location : Paris, France
Admission: Free. The greenhouse require an entrance free.
Review:

On a sunny day, Jardin Des Plantes is a less crowded park compared to the parks near Eiffel tower. I was delighted to know that the botanical garden is open free to all. A fee is required to enter the greenhouse. There is no way I'm paying money to see banana and palm trees! The botanical garden is well-maintained and organized. The plants are sorted into different sections according to their families. All the plants are well-labeled and descriptions are sometimes provided, however, in French. I spent about two hours there. Before leaving, I sat down on the bench to wipe my shoes because the walkway was sandy and dusty. A highly recommended place.

Clockwise from top left: Garden overview, sandy walkway and green house.

Clockwise from top left: Cherry blossom, poppy flowers and Medicago sativa. 

3. Keukenhof Garden
Location: Lisse, The Netherlands.
Admission: EUR 22.50 (Entrance + bus ride from Leiden trainstation)
Review:

Although Keukenhof is not a botanical garden, it is a place not to be missed in spring if you ever go to The Netherlands. The overwhelming recommendations about this place has made me skeptical at first. Honestly, this place is not overrated. It is the MOST BEAUTIFUL & COLOURFUL garden I have ever been! There is no other places like this on earth. I'll let the photos do all the talking. 

Besides tulips, there are colourful arrangements of hyacinth, daffodil and narcissus and some other flowers. I also visited the two exhibitions on arts, orchids, kalanchoe and hippeastrum. I spent about two hours there (which is enough if you're not taking photos crazily). Do bring company because you wanna take many nice photos of yourself. If you have more time, you can rent a bike and explore the tulip farms around the garden. 

 Tulips in Keukenhof garden.

Keukenhof garden, pond and exhibitions.

4. Botanical garden by The University of Utrecht
Location: Utrecht, The Netherlands
Admission: Free admission
Review: A small garden maintained by the university. It's worth having a look if you ever go to Utrecht.

 Botanical garden by The University of Utrecht 

5. Hortus Botanicus, University of Leiden
Location: Leiden, The Netherlands
Admission: EUR 7
Review:

The oldest botanical garden in The Netherlands. I didn't get the chance to go inside because I had very little time to spend in Leiden. I can see a garden and a green house from the main entrance. There are several types of tulips at the main entrance as the theme was tulip at the time of my visit. 

6. Botanical garden, University of Potsdam
Location: Potsdam, Germany
Admission: Unknown. According to one website, it's EUR 2 which is too good to be true.
Review:

Potsdam is an UNESCO heritage site that you can't miss when you go to Berlin. The botanical garden is located within the beautiful Park Sanssouci. I think tourists need to spend two full days to explore all of what Park Sanssouci has to offer. I didn't visit this botanical garden due to time constraint, however, I passed it several times. 

Botanical garden, University of Potsdam (Image source: Wikipedia)

7. Palm Garden at Hofburg palace
Location: Vienna, Austria
Admission: Unknown
Review -

It was a rainy morning when I went to Hofburg palace. I was surprised to find a palm house in the city centre. The palm house is located right next to the butterfly house. It looks like the Austrian royal families love palm houses! I didn't go in because I was never a big fan of green house and palms (I see them every day). 

Palm Garden at Hofburg palace

8. Gardens at Schonbrunn palace
Location: Vienna, Austria
Admission: Depends

There are many gardens in Schonbrunn palace such as the botanical garden, palm house, Crown Prince garden (Admission 3), Maze & Labyrinth (Admission EUR 4.5). However, a fee is charged to go in. I think all the gardens were blocked from the visitors' views by tall trees and scrubs.  According to the official site, the botanical garden was turned into English style garden. Since there are many beautiful sights around the palace such as the fountain and buildings, I wouldn't recommend spending extra to get into these garden if you only spend one day at the palace.

 Schonbrunn palace garden

Other sights in Schonbrunn palace garden

9. Botanical Garden, University of Vienna
Location: Vienna, Austria
Admission: Unknown
Review:

This botanical garden is located right next to Belvedere palace. It was constructed in 1754 under the order of Empress Maria Theresa. The entrance can be hard to spot as it was a bit hidden. From the main entrance, I can see two paths leading into the botanical garden. A few joggers were spotted. The plants near the ticket counter looked healthy and well-labeled. According to Wikipedia and Gardenvisit, the botanical garden looks quite big and consists of several greenhouses but not open to public. Unfortunately, I didn't have time to visit this place because I had to catch a train to Florence.

Top: palace garden view from Upper Belvedere; Bottom: Botanical garden, University of Vienna

10. Boboli Garden at Pitti Palace
Location: Florence, Italy
Admission: EUR 13
Review:

This garden which is located in Florence used to belong to the rich and powerful Medici family. The Italian garden seems to consist fountains and many sculptures. I caught a few glimpses of it from the Pitti Palace window. The ticket price is the same price as the palace and the combo ticket is not much cheaper. 

Views of the garden from Pitti Palace

Read more...

Concerns on the graduate student dropouts in Malaysia

This topic has been lingering in my mind for awhile now. For the past few months, I talked to several students regarding their choices to drop out of their graduate programs. My 4-year PhD experience tells me that at least half of the graduate students in life sciences never complete a degree. I tried to make a list of students I know who dropped out of graduate school. I stopped counting at ten because the list just gets longer and longer. Majority of them quitted during the first year of involvement. I would use the word “involvement” rather than referring to a formal graduate program because some students stopped before starting a research program. These can be students who are preparing research proposals or working as a research assistant for 6-12 months with the intention of doing a postgraduate study.

Let’s look at some online facts

• The dropout rate for postgraduate students are generally around 50% and lower in science subjects
• According to Chronicle of Higher Education (2004), 37% of students who begin PhD never obtain the degree.
• Women drop out at a higher rate than men (Chronicle of Higher Education, 2004).
• Around 25-29% of PhD students in life sciences dropped out according to Elearners.com.
• No comprehensive national statistics is available in Malaysia. In 2011, New Straits Times reported that 3 out of 10 part-time PhD students never complete due to work and family problems.

The number of years before you think you can graduate

Why students hesitate?

1. Timely completion. I think slow progress or not getting the expected results is the main reason why many students gave up. They might think that a specific task is too daunting or impossible to complete. They do not have confidence in overcoming the problems or getting help from others. In addition, some students hold unrealistic expectation to complete their degrees within a short period of time, say three years sharp for a PhD. They might be afraid of financial or visa problems if they do not complete within time. This eventually gives rise to other problems because more importance is placed on speed rather than quality of the research.

2. Commitment and interest. Most students want to join a postgraduate program because they are interested in science and research but that interest can change over time. Some might want to improve the chances of finding a job, some dream of getting a higher degree and some hope to work in the academics. They might find that doing a postgraduate program is no longer suitable. They did not obtain the results or  satisfaction they expected. They might join a program without fully understanding it and leave when they fully understood it.  

3. Money. Money is the problem in some cases. I think that stipend and debt such as study loan pose very little problem because postgraduate students in Malaysia usually receive a monthly stipend more than sufficient to cover their living expenses and tuition fees. A lot of students worries over grant and research funding. Is it going to run out soon? Will I be able to buy the kits and consumable needed? Will the grant able to support me until I graduate?  I think it is supervisor’s responsibilities to obtain grants and ensures the students that they will have sufficient materials, resources and financial support to complete a degree. When the students think that  there is nothing they can do, they choose to leave.

4. Interaction with supervisor. The quality of relationship between student and supervisor is often cited as the heart of the problem. It will take several years to foster good relationship and trust between the two parties. This relationship is usually weak during the first year when most dropouts occurred. One common problem I spotted is students are often too timid to discuss problems with their supervisors and worry too much of what their supervisors might think.

5. Pressure to publish. Nowadays students faced increasing pressure to publish their researches because publishing has been made compulsory to graduate. In UKM, Master and PhD students are required to publish one and two papers respectively in scientific journals. Some of their worries are related to timely completion, getting enough data for a publication and fear of being rejected by a journal. I strongly support this policy because most students who graduated without publishing never publish. In addition, I think publication will give the students greater satisfaction and motivation to thrive in their researches.

6. Family.  Family commitment, getting married and starting new family are some reasons students dropped out of graduate school. Some students especially young ones find it difficult to cope with family and studies simultaneously. Few might need to sacrifice their studies for their spouses. Only the determined students who received great family support can successfully completed their studies. Based on my personal observation, students with family commitment who are sponsored by an institution or company to pursue a higher degree are less likely to drop out but most likely to extend the semesters.

My advices for the hesitating

•  Identify what makes you hesitate
• Think about why you want to get a Master or PhD degree. Do you still want it now?
• Seek advices from your supervisor early on. Once you have identified the problems you faced, I strongly recommend that you let your supervisor know so he/she can help you.  
• Seek advices from other graduate students. They are often more than willing to share their personal experiences, give technical advices and tips on how to improve communication with your supervisor and others.
• Take a holiday if you find that work is stressing you out a lot. It’s time to take a break if you keep repeating a certain experiment and unable to get any result. It is important to have a well-balanced work and life.
•  Get emotional support from friends and family. Let them understand that doing a postgraduate study can be a long and stressful process.

Possible future solutions

Some solutions to reduce the high dropout rates in PhD students have been proposed in the articles I read online. First, there is a need for proper statistic on the actual number of PhD dropouts. A problem well-defined is a problem half solved. Another suggestion is to choose only the best student for PhD programs. The percentage of students completing a PhD increases to 70-75% after vigorous selection of the scholarship committee. In China, students are required to take an entrance exam to enroll into postgraduate programs from the Chinese Academy of Sciences. This is similar to Graduate Record Examinations (GRE) which is compulsory to pass for all international students before joining universities in Singapore and United States. One author suggested that sufficient training in time management and manuscript/thesis writing will curb the problem. One of my suggestions is to strengthen bonds and relationships between postgraduate students through activities organized by the graduate student association. In order to prevent dropouts under the Graduate Research Assistant (GRA) scheme, perhaps there is a need for the students to sign a contract which requires compensation if the student did not complete the study.

The scenario of life sciences research in Malaysia is changing rapidly over the past few years. Nowadays principal investigators are more concerned about meeting milestone deadlines, pressure in publishing and competition in grant writing. A few years ago, it is very rare to hear that a postgraduate student was fired due to poor performance but I expect things to change pretty soon. 

Read more...

Danum Valley retreat (15-18 Oct 2012)

Danum Valley is a large forest reserve owed by Yayasan Sabah located in Sabah, Malaysia. It is part of the large piece of rainforests given by the Sabah government to Yayasan Sabah. About 14% of the land was reserveed as  forest conservation area while the rest was logged in the past. Danum Valley aims to cover half of its expenses using revenue from eco-tourism.

I was very fortunate to visit Danum Valley from 15- 18 Oct 2012 for a retreat with my supervisor and labmates. We were invited by one of the co-founder, Mr. Cyril Pinso to visit the facilities. The fastest way to get to Danum Valley is to take MASwing flight from Kota Kinabalu to Lahad Datu airport and then 1.5-2 hours 4WD drive from the airport to Danum Valley. Danum Valley is largely unknown to many Malaysians, at least not until Prince William and Duchess of Cambridge visited it on 15 September 2012.

Upon arrival at around 7pm, we checked in at the reception building. We were informed that there is no phone reception and internet connection (except for a very expensive fee). Electricity is only available from 7am to 12am midnight. Breakfast, lunch and dinner are available in the cafe at 7am, 12pm and 7pm respectively. Drinking water, tea, coffee, snack are available in the cafe. Packed lunch can be arranged upon request. 

Facilities at Danum Valley (clockwise from top left): cafe, laboratory, reception and view in front of resthouse

The facilities at Danum Valley include reception, cafe, laboratory, staff houses, hostels and resthouse. There are two types of accommodation, namely resthouse and dorms. There are 8 rooms in the resthouse which is located right next to the cafe. There are female and male dorms, each consists of 80 beds (if not mistaken). The dorms are close to the staff housing area and football field, about 10 min walk away from the cafe. The room facilities in the resthouse exceeded my expectation! Towel, toilet tissue, kettle and cups were provided.  Since hot shower is not available, I have to use the kettle to boil water because the water is quite cold. The accommodation rates are affordable but a more expensive rate applied to all international visitors. 

Some of the interesting activities to do are jungle trekking, night walk and sunset/sunrise tour. There are several trails that can be explored such as nature trail, orchid trail, coffin trail, Tembeling waterfall trail, a 6-day trail to Borneo Rainforest Lodge. All trails except nature trail and orchid trail requires a guide. Borneo Rainforest Lodge is a high-end nature resort located near Danum Valley. An attraction near the Borneo Rainforest Lodge is the tree canopy walk. There are several tours available such as night drive tour, sunset and sunrise tour. A 4WD has to be hired for the tours and therefore, it will be better to have at least 4 persons to share the cost. 

On the second day, we explored the coffin trail together with a group of German tourists in the morning. The trail was named coffin trail because a burial site with ancient wooden coffins can be found at the end of the trail. The patterns carved on the coffin resemble Chinese patterns and furthermore, these coffins were located right next to the riverbank, suggesting Chinese origin. First, we crossed the Segama river using a hanging bridge and walked about 2 km to get to the burial site. The burial site also consists of vases and potteries. The coffins were so much smaller than I expected. 

Coffin trail

After completing the coffin trail, we walked back to the cafe for lunch but we stopped at the sights of ORANGUTAN!!! One female adult with a baby were spotted at a rambutan tree right in front of the resthouse. The mother was eating some raw rambutan fruits while the baby was waiting. Initially the baby was trying to catch up with its mother. After 15 min, the baby looked bored and tired so the mother carried the baby and went back into the forest. Observation of the interaction between the mother and child is an amazing experience because their behaviour resembles human behaviour a lot. The first time I saw an wild orangutan! 

Adult orangutan with a baby spotted at a rambutan tree near the cafe

In the afternoon, we explored the nature trail on our own. Nature trail is a well-maintained trail with signboards close to the resthouse. We stopped by the viewing platform to take some photos. At the end of the trail, we saw the tree platform but unfortunately, it was closed for maintenance. After walking the trail, some labmates and I went to the small river behind the cafe to chill out. We then had dinner and retired early for the day. 

On the third day, we woke up for a sunrise tour at 5am. We were picked up by two 4WDs to a viewing platform. We climbed up to the platform and waited in the dark. At this hour, the forest was covered in thick mist. As the sky brighten, the noises of the birds and animals got louder. The first beam of sunlight slowly appeared from the horizon and turned the sky into red flames. But in the next few minute, the sun quickly emerged from the clouds. We were able to see the big and round burning sun hanging above the forest and clouds for a few seconds before the sun became too glaring for our naked eyes. 

Sunrise tour

After breakfast and a short rest, we decided to go to the Tembeling waterfall. The trail is about 6 km return and poses  more challenges compared to coffin trail and nature trail. When we finally reached the waterfall, we had to take off our shoes to cross the river. The waterfall is a decent waterfall with about three-storey height. Some of us climbed over slippery rocks to stand under the waterfall. There is a small catchment pond with water level up to my waist. We spent some time playing with water before we headed back to the resthouse. 

Tembeling waterfall

After dinner, all the guests were given Powerpoint presentation to introduce us to the history of Danum Valley. Then, I followed one tourist on a night walk around the facilities in search for night animals. I was very fortunate to spot a mousedeer, two types of civets and a large frog. It is an eye-opening experience and made me realized that night walk is the best way to spot the animals. 

The whole experience in Danum Valley was amazing. 3D2N was too short a trip. It is the first time I have been up close and personal with so many wild animals. These animals were roaming freely near the facilities and were used to human presence. I would definitely recommend this place to all nature lovers.

Read more...

Sexual harassment : The hidden danger for female graduate students

What is Sexual harassment? 

There are many definitions of “sexual harassment” online. As Malaysians are largely conservative about sex, the most common form of sexual harassment is verbal harassment. I find the most accurate definition to fit into this context is 

“any form of unwanted verbal, non-verbal or physical conduct of a sexual nature occurs, with the purpose or effect of violating the dignity of a person, in particular when creating an intimidating, hostile, degrading, humiliating or offensive environment”

Why am I writing about this? 

Sexual harassment can happen in the campus. In many reported cases, the sexual harasser holds a higher position (i.e. a faculty member) and has certain power over the victim. However, I would like to focus on this issue amongst graduate students. In this stage, most graduate students are in the range of 23 to 30 years old, mainly single. Some are probably lonely and desperate to get married. Some students are under a lot of stress from study and life. When they face rejection and criticism, they take their frustration out on the victim. Keep in mind that a married man can also be an offender. 

I know three cases of sexual harassment: 1) A female student was proposed by a staff several times. He was transferred to another place after she made formal complaints (Specific details not known as I heard this from a friend); 2) A female friend was harassed and stalked by a male student that I know. He kept persuading her to take his present and go out with him. He also kept sending emails and even implied that he wants to marry her. 3) The third case is my personal experience.

My long story short. The sexual harasser is somebody i called a colleague for 4 years (and a friend!). Last year I found out that he likes me but I never have any romantic interest in him. I have tried to remain friends because I didn't want to hurt his feelings. Two months ago, he made his second attempts to provoke me and I emailed him to say that we’re no longer friends. To my surprise, he thought that I want to be his girlfriend! So I emailed him firmly stating that this must be an understanding and gave several warnings if he want to pursue this further. He replied me angrily with “Go to hell” and I have never reply him since. During the past 2 months, I only saw him several times in the library as he no longer going to the lab. Just three weeks ago, he emailed my supervisor questioning why I did not invite him to lab meetings (totally baseless accusation).  He also forwarded my past email/s to my supervisor and another student in an attempt to to sabotage my relationships and credibility. He also sent an email and sms to intimidate me. I felt like I can no longer keep quiet about the whole incident and so, I wrote my supervisor a long explanation email together and forwarded his past emails as proof. My supervisor assured me that it will be taken care of and asked me to focus on my work. I'm really lucky because my supervisors and friends are so supportive. Unfortunately, I don't think this is the end of it. 

How to recognize sexual harassment? 

Below are some conducts and types of sexual harassment from this pdf file.

• Actual or attempted rape or sexual assault (physical)

• Unwanted touching and kissing (physical)

• Giving personal gifts in exchange for sexual favours (non-verbal)

• Staring, following (physically or on FB) or stalking the person (non-verbal)

• Asking for sexual favors (verbal)

• Unwanted letters, phone calls, emails or sms of sexual nature (verbal)

• Repeatedly asking out a person who is not interested (verbal)

• Unwanted sexual jokes, questions and comments (verbal)

• Calling somebody as babe, honey and dear (verbal)

• Telling lies or spreading rumors about a person's personal social and sex life (verbal)

What are the available online resources?

The important resources I found online online are:

1) Blog on Being A Woman in Philosophy

I found some of the stories shared are horrible examples of sexual harassment but nonetheless, very useful. This blog has resulted in some serious debates at Metafilter (see link to post).

2) Susan Gardner

I found the most useful article written by Susan Gardner (see link to article), a victim of sexual harassment in during her graduate study. Now as an associate professor, she promoted awareness in sexual harassment and encourage victims to step out. 

3) Blog on Sexual Harassment Against the Law

This blog was created by UKM students covered a broad range of topics including Malaysian law against sexual harassment. There are two types of legally recognized way of committing sexual harassment: (1) Quid pro quo sexual harassment; and (2) Hostile environment harassment. The effects of sexual harassment on the victim was adequately highlighted. According to The Penal Code, section 509,

"Whoever, intending to insult the modesty of any women, utters any words, makes any sound or gesture or exhibit any object, intending that such word or sound shall be heard, or such gesture or object shall be seen by such woman, shall be punished with imprisonment for a term which may extend to 5 years or with fine, or with both".

4) All Women's Action Society (AWAM) guide on sexual harassment

AWAM is onne of two NGOs on the government’s Technical Working Committee that produced the Code of Practice on the Prevention and Eradication of Sexual Harassment in the in the Workplace that was introduced in 1999. A 2002 study conducted by AWAM and Women’s Development Collective (WDC) found that 35% of respondents in Malaysia had experienced one or more forms of sexual harassment. Together with the Joint Action Group for Gender Equality (JAG) AWAM campaigns for the enactment of a Sexual Harassment Act. They also publish a article about Myths of Sexual Harassment in Malaysia. 

5) Pdf file of Guide to Sexual Harassment (Malaysia) from Lawyerment.com.my

6) Assoc. Prof. Dr. Sabitha Binti Marican from Universiti Malaya

Sabitha, M. & Khadijah, M. (2004). Understanding and Managing Sexual Harassment at Higher Leaning Institutions: A Malaysian Case. Proceeding Management Education Excellence: The New Frontiers, Universiti Utara Malaysia. 

7) Assist. Prof. Dr. Patricia Sloane-White from UTAR

Research interest in sexual harassment in Muslim corporations

Some universities such as Harvard University have guidelines and procedures for sexual harassment including a list of officers to be contacted (see link). A search in Pubmed about “graduate sexual harassment” returned 41 hits. Less than one third of the articles are relevant. I only found four titles that are highly relevant but half of the studies were conducted in 1990s. Does this show how little this problem is addressed in academia?

How to prevent it?

First, you need to recognise when you're harassed. In the beginning, the student will attempt to ignore the incidents and hope that those uncomfortable feelings will go away. Like what people say, "out of sight, out of mind". Unfortunately, most harassers stick around and caused more damage to the victim's mental health. Second, tell the harasser that you don’t like his actions and that you want him to stop. If he wants to date you, you must firmly state that you’re not interested. Do not give vague excuses. Tell him he’s not your type and you’ll NEVER be interested in him. Never try to be friends or friendly with him (that's my mistake). Try to avoid him whenever possible. If you're somebody confident and comfortable around others, you might be misunderstood by your male counterpart as showing an interest in him. The sexual harassers that I know are overly sensitive guys who tend to overthink and misinterpret a girl’s intention. For example, when you say no, he might think you’re playing hard to get, just upset or jeolous. Do not allow room for his imagination. 

If sexual harrassment happens to you, what do you do? 

Some suggestions from my own experience, supervisors and online resources.

• Tell the harasser that you don’t like his actions and that you want him to stop. To avoid any miscommunication, make sure you be clear and direct. Don't apologize or smile.

• Consult your friends who will listen to you. Only cry in front of the friends you trust.

• Avoid your harasser. Hide somewhere until things cool down

• Always keep EVIDENCES- whether it’s a sms or email. Don’t delete it just because you’re angry, upset or scared! I was sooo thankful I still keep the harasser's email that said he likes me. Otherwise, it’s his words against mine!

• If somebody else is present during the incident, ask that person if he/she can testify against the harasser.

• Keep a written account of the harassment including date, time, the harasser’s name and how the incident(s) happened.

• Do not reply. If you have to, reply after you’ve calm down and think over what you want to say. Be careful with what you say as you might need to show others as evidence.

• Put on a brave face if you have no choice to avoid him. Do not show him that you’re affected by his actions.

• Consider discussing this problem with a senior position outside of your institution. In my case, my co-supervisor was the first few people i talked to and receive support from.

• Consider informing your supervisor. First, you need to know what is his/her reaction to your story. They might need some proof or evidences to be convinced and probably need to consult somebody of higher position.

• If things get very serious, consider filing a formal complaint to the dean and university. In this situation, be prepared to be interviewed. If you feel like you’re about to cry, don’t restrain yourself. You need to show them how much it has affected you before they take you seriously.

• Call AWAM (Telenita helpline: 03-78770224; email:awam@awam.org.my) or a women’s NGO for help and guidance.

• Worst case scenario - make a police report. You might consider hiring a lawyer to pursue a civil suit.

Conclusion

I hope that my post will create awareness among graduate students. Some might not be aware that they're harassed or even harassing other people. Most victims suffered in silence because they do not make formal complaints. Out of the three cases mentioned, only the first case was formally reported. Some victims hope it will go away soon while some feel sorry or guilty to report the incident. The latter is exactly how I feel in the beginning. However, you must remember that what you go through is not your fault, it's his! Reporting it is the only way to prevent creating another victim (ya that's being said back to myself). In addition, there is a need for clear guidelines and implementation for local universities in Malaysia. There is a clear guideline for chairs or academinc staff from higher position on how to handle sexual harassment (see link to website).  Students needs a support or counselling group where they can share their personal problems. Furthermore, a recent newspaper article in The Star discussed the need to pass the Sexual Harassment Bill to protect women from workplace sexual harassment. We must be preparing for it before it happens.

Read more...

Launching of Mycite or Malaysian Citation Index

As the editorial assistant of Malaysian Applied Biology Journal (MABJ), I attended the launching of Mycite on 22 May 2012. The launching ceremony was officiated by the Minister of Higher Education, Yang Berhormat Dato Seri Mohamed Khaled Nordin and followed by International Conference on Journal Citation Systems in Asia Pacific Countries. Honestly, I was very blur before I attended this event. I was told that there are some talks but I wasn’t aware that a conference will be held. Not long before that, I found out that MyJurnal (a part of Mycite now) has included abstracts from MABJ in its website. The chief editor almost thought that the journal has been sabotaged but fortunately, one of the associate editors explained that MyJurnal is an initiative by MOHE.
                                               

What is Mycite? MyCite or Malaysian Citation Index is an initiative by MOHE with objectives to a) To improve journal publication in Malaysia; b) To improve rating of Malaysian publishers; c) To list all Malaysian journal publications; d) To measure the scientific impact of Malaysian journals; e) To increase global visibility of Malaysian publications. MyCite covers all fields in Science, Technology, Engineering, Medicine, Social Sciences and Humanities. It is linked to Myjurnal. In the future, Mycite aimed to form ASEAN Citation Index with other countries and to suggest Malaysian journals for Scopus evaluation. In simple terms, I think we can say that Mycite is a database similar to Scopus and Thomson Reuter Journal Citation Report that was developed for Malaysian higher education, researchers and journals.

History of Mycite. Mycite was adopted from MyAIS (Malaysian Abstracting and Indexing System from UM). Malaysia Citation Centre (MCC) was established in Universiti Malaya on April 2011 to develop MyCite. More details available at link.

Significance of Mycite to authors and publishers

• Authors can search for articles published by local journals using Myjurnal
• Authors can check the articles they have published in local journals
• Authors can check who is citing their work
• Publishers can find out their journals impact in 2 and 5 years window, h index and immediacy index.

International conference on Journal Citation Systems in Asia Pacific Countries

After MyCite launching ceremony, nine speakers from Southeast Asia and other part of Asia presented their work on citation database, namely Malaysia, Thailand, Philippines, Indonesia, Japan, Taiwan, Korea and China. Out of these, only one speaker is affiliated with private company.  I think the most interesting talk is given by Prof. Dr. Narongrit Sombatsompop from Thailand. The Thai-Journal Citation Index (TCI) was established about 10 years ago and has made great archievements, i.e. producing publications and organizing conferences. In addition, it’s a privilege to listen to Prof. Dr. Su Xinning from Nanjing University, China. He developed the first citation index in China in 1989 which has been used as a model in citation database for many countries. I'm amazed that I stayed awake during all the talks which are very similar and doesn't relate much to me. Generally, I think the whole event is a great success. It has provided a great platform for publishers to network besides learning more about citation database. It has gave me an opportunity to speak to Prof. Dato’ Dr. Looi from UM and found out about APAME 2012. Details as follow:

Asia Pacific Association of Medical Journal Editors Convention 2012 (APAME 2012)

Theme: New Horizons in Scientific Writing and Publishing

Venue: University of Malaya, Kuala Lumpur, Malaysia

Date: 31 August - 3 September 2012

Registration fee: USD120 (local) & USD 250 (overseas)

website: http://ammje.org/apame2012/

There are three Post-Convention Workshops which cost USD50 each: 1) Keeping standards high - how to be a reviewer; 2) Evaluation journal; 3) Bibliography managing - Enduree & Mendely. I find it rather strange to pay to attend a workshop on how to become a good reviewer as most reviewers did not get paid.

Read more...

Should I publish a conference proceeding?

I’ve been asking this question several times this year because I happened to be interested in attending conference/symposium/seminar which requires full paper submission. Honestly, I’m confused because I have only been asked to submit abstract for the past conferences I’ve attended. Some of the common fears or uncertainty are exposing too many details in the full paper submission and publishing work in a proceeding rather than a journal. 

Early this year, my supervisor asked me if I would like to attend the InCoB 2012 Conference in Bangkok, Thailand. One student from our group attended the KL conference last year and subsequently published a proceeding in BMC Genomics (Impact factor: 4.21). I wasn’t keen at first but the idea of having another publication in BMC Genomics definitely sounds appealing. On second thoughts, I do have some unpublished data but it will require a lot of time to analyze them and write a full paper. In the end, I decided not to join because I will risk missing my manuscript and thesis deadlines. 

What is a proceeding?

According to “Articles vs. proceedings papers: Do they differ in research relevance and impact? A case study in the Library and Information Science field” by Gonzalez-Albo & Bordons 2011, a proceeding is defined as a paper that was presented at a conference and later adopted as a publication in a journal. It is usually shorter than a journal article and may not be suitable for journal publication. The authors choose to publish the results from proceeding in a journal to increase visibility and citation. In medical fields, only 30-50% of the proceedings were published as journal articles.  It is important to note that a proceeding paper should not be viewed as having lower quality and relevance compared to a journal article. However, it’s undeniable that a journal article is valued more than a proceeding paper in the academics. Proceeding papers are published faster than regular journal article but this has become a thing of the past. 

Why publish a proceeding? 

I found no clear answer until I read this blog in Survival Blog for Scientists. Here’s what I can summarize on the reasons to publish a proceeding:

• Providing a sense of community

• Addressing the relevant people

• Getting one’s work known and acknowledged

Why not to publish a proceeding?

• A waste of time. Why not use the time to write a manuscript for journal publication? 

• Low visibility and citation. Most proceedings are not indexed in databases. 

• Bad for your CV.

How to avoid publishing a proceeding?

We all want our research to have high impact so some of us might not be interested in publishing a proceeding after attending a conference. Some conferences will only select a number of papers based on quality assessment and thus, not all authors faced this dilemma. Even if a conference requires full paper submission, the authors especially students are often not aware that they can avoid publishing a proceeding. How? Easy. If you don’t respond, your paper will not be published!!! Haha I have to admit that this is not a very professional thing to say. Well, you always have a choice not to go! 

Conclusion

It’s clear which side I have taken in this topic. Honestly, I think that a conference abstract will be sufficient serve the purposes of a proceeding mentioned above. Considering the disadvantages of publishing a proceeding, we should invest our time in more useful stuff. In addition, I would like to point out that I dislike the practise of some conferences in publishing the proceedings before the conference is held. I rest my case!

Read more...

Books related to tropical forestry and genetics

Just a few days ago, I was feeling a bit bored so I looked up at Springerlink for books related to forestry. I found some quite interesting ones that I would want to read (if I had the time) and share. I added a few books from other publishers to the list. So here the list of 7 books related to tropical forestry and genetics (sorted according to the year published). I've only read three of these books, two which are available in the UKM's library. Another two books (No. 3 & 6) can be read online for free! My favourite is "The Ecology of Tropical East Asia" by Richard T. Corlett. It was so interesting that I finished reading the book in a week during my holidays last year. Enjoy!

1. Managing the future of Southeast Asia's valuable tropical rainforest : a partitioner's guide to forest genetics by Wickneswari Ratnam & Chuck Cannon, 2012

2. Tropical Islands Biodiversity Crisis by David J.W. Lane, 2011

3. Genetics and Genomics of Populus by Stefan Jansson, Rishikesh Bhalerao and Andrew Groover, 2010

4. The Ecology of Tropical East Asia by Richard T. Corlett, 2009

5. Tropical Forest Genetics by Reiner Finkeldeny, H.H. Hattemer, 2007

6. Plantation Technology in Tropical Forest Science by Suzuki, K., Ishii, K., Sakurai, S. & Sasaki, S., 2006

7. Origin and Evoluation of Tropical Rain Forests by Robert J. Morley, 2000

Read more...