Festival of Plants 2015

Yet another of my free writing :)

I went to the Festival of Plants in Cambridge University Botanic Garden last Saturday. A nice sunny day to be out there among the beautiful spring plants. Our first stop was the canopy where there were stalls with interactive games and explanations provided by volunteers of Festival of Plants. One thing which attracted me was the booth on algae and biofuel. I work with Chlamydomonas reinhardtii, one of the few algae studied widely on its ability to produce biofuel, and I do like the idea of this animal-like single-cell lower plant being such a useful tool to study various aspects. We created a furry cartoonish ChlamyBaby (look below). There are some other activities which I didn't stay long enough to gather info. However, it seemed to me that people were enjoying themselves. We passed by the glasshouse and there was an interactive concert going on. Nice vocal for sure!

There were tours around the gardens, according to my friend, it was very beneficial as the guide told the stories of many of the trees around the garden. There was a talk tent where various talks were conducted. Apparently they were good too.

ChlamyBaby wading on the grass

I managed to capture a few nice shots - thanks to the lovely afternoon sun!

Moor hen feeding her chick

Colourful tulips

Peony?

Iris

I had a great time that afternoon. Discovered it was my friend's birthday, which was nice. Since the weather was great! :)

Scientific Walk in Romantic Sintra

I went away last weekend to refocus and refresh before this hectic season. I'm in the process of writing my first year report, but at this moment, I am kinda frozen in time and space. So, as what the trainer of the Graduate School of Life Sciences (GSLS) suggested, I begin a short piece of free writing on some random topic.

Finally, I was in Sintra. After pondering for a few nights on which part of Sintra I should do and how much I was willing to spend, I've decided on Castelo dos Mouros (Moorish Castle) and Parque e Palacio Nacional da Pena (Pena National Palace and Park).

View of Palacio Nacional da Pena from Castelo Dos Mouros at the spot where King Ferdinand II loved as he found it an inspiration for his romantic ideals.

My favourite picture of the Castelo

It was an amazing journey and I did take many excellent shots of the breathtaking views, and plants! I never thought I'd end up in the Dept of Plant Sciences, but since I'm already in it, I should make the best out of it. I may be a ChlamyScientist working on molecular biology/physiology of Chlamydomonas reinhardtii, but my colleagues are great physiologists/ecologists. I'm beginning to see beyond the green and to see each plant as a different species. It will take time, but I hope I can make my way closer to them greenies.

Navelwort I think... also in Parque Nacional da Pena

Sedum sp. in Parque Nacional da Pena

Fascicularia bicolor, a Bromeliad in Castelo Dos Mouros

Keep Calm and Start Writing!

How apt is this "keep calm" phrase!

Some of my friends have begun writing their theses, some had completed and submitted. As for me, I am just starting my PhD journey (finally!) when I joined this lab (Physiological Ecological Group). Looking at how four months flew off like lightning, I should begin writing the first year report soon since the deadline is on 1st June.

The reluctant mind and body says, "There is still time. Chillax!" But both know better that it is only a lie. One thing would lead to another, and there are thousands, if not millions of papers I need to wade through in order to seek for the knowledge. I have yet to start writing the ONE word needed for me to begin.

It's time to think. It's time to start writing. I shall.. Within this week. Now, I shall give my pair of fatigues eyes a rest. Ciao!

Coffee and Graduate Students

As I venture deeper into the journey of a graduate student, I find that coffee becomes a part of my life, as much as I don't want to be "addicted" to it. I'm trying to deny the fact that I might be a coffee addict at heart, refraining myself from overdosing since the forensics background I've accumulated reminds me anything too much isn't good for me. So far, I'm fully aware that any caffeinated drinks from Nescafe would cause me drowsiness. I suspected the case when I tried staying awake to study using Nescafe Gold (yes, I only go for the best stuffs) but I ended up sleeping for hours after that cuppa. It didn't help me to study more, but my body was indeed well-rested due to the blood-pumping caffeine.

When I speak to my graduate friends, I noted that almost everybody (shy those who are allergic to caffeine, and those who drink tea like water) would have at least a cuppa a day. Some would be at the extreme of consuming more than 6 cups daily. On average, about 2 to 3 cups. As for myself, it is once a day, in the morning when I have my breakfast, usually around 9ish. Today I woke up late so I got my brunch by 11am. According to this website, the best time to drink a cuppa coffee is between 9.30 am to 11.30 am.

The initial realisation came when I stopped by Costa in Grand Arcade daily to grab a cuppa on my way to the department. I tried to be more environment-friendly, so I bought its travelling mug. Uh-huh... it stuck with me for two weeks, and I noticed how my purse bled to death. I am but a poor scholar, honestly. Money should be spent on real, filling food. So I had to think of alternative... While Costa can be my choice when I hang out with friends. Always - the hazelnut flavour!!!!

Source: http://upload.wikimedia.org/wikipedia/en/thumb/4/42/CostaLogo.svg/1024px-CostaLogo.svg.png

I was deciding between a coffee maker and a cafetiere. I chose the latter, not because I couldn't afford it but due to the fact I don't have much table top space to keep it. A stainless steel Grunwerg 3-cup cafetiere quenched my thirst of brewed coffee. Adorably shiny little thing that my heart fell in love with. Got it from Amazon using the prize money I got for being the kid with best performance of my MSc. degree. Wheeeee!!! Now I can have non-instant coffee at home. Whenever I want to.

Source: http://ecx.images-amazon.com/images/I/21ovJ5WYYcL.jpg

Initially I stick to ground coffee from Costa, as much as I like it fresh, it's not the same as what I get in the shop. Of course, no frothy milk to accompany with it does make a difference. That's when I re-discovered my love for OldTown White Coffee (hazelnut flavour) from my home country, Malaysia. Yet, a pack only consists of 15 sachets, and I died when I found I was left with one sachet the first time my ex-student brought my "supply" from home. Thank God for my kind-hearted best friend who came back for his graduation, I received two packets. And from a friend who finished her Mphil, I inherited her leftovers. Yippee!! That will keep me going for a while. But I need to look for alternatives...

Source: http://i01.i.aliimg.com/wsphoto/v0/669333435/Malaysia-import-old-town-Old-Town-White-Coffee-Hazelnut-flavor-instant-3-in-1-600g-horse.jpg

One random shopping day at Tesco Extra in Bar Hill, I saw this lovely red packet of ground coffee with the label "Hazelnut". I don't know much about this Edinburgh Tea and Coffee Co. but I supposed the price reflects on its quality. It was priced at £3.70. Not expensive, but higher priced than others. I finally made the first cup today. Completely took my heart away. I've found the non-sugary alternative to my OldTown White Coffee.

Source: http://coffee4.me/wp-content/uploads/2014/04/Edinburgh-Tea-and-Coffee-Company-Hazelnut-Ground-Coffee-227-g-Pack-of-3-0.jpg

So, I shall continue my work now. Till then... Have a cuppa!


P/S: Many would agree with me, right??

Source: http://phdcomics.com/comics/archive/phd070513s.gif

PLINK for Windows

As I'd have to pay for every Gigabyte of internet used, I was a little concerned about working in the comfort of my room. The move to a room with larger window overlooking the backyard where a couple of squirrels and a pair of pigeons reside at the pine tree really helps with a better working at home environment. I'd need to work in the department once in a while, but the alternative is as good as the office, so I feel comforted. And finally, a more sturdy desk chair is provided to me today! Yay!

This is the view from my desk: perfect, isn't it? Getting back to work :)

Back to the topic, since I'm using a laptop installed with Windows 8.1, I was thinking of running PLINK on the laptop, provided I have enough HDD space and RAM, of course. I think with 6GB of RAM, I should be able to do quite a bit before I crash it. A tiny search on PLINK website led me to the MS-DOS version of PLINK, which means I could do the genomic analysis offline without using my group's server! Another yay!

Here's the instruction as per PLINK website on how to download and install PLINK on Windows... I think the links on my page would lead you to the download site, further instructions and manuals for PLINK. Enjoy using the whole genome association analysis toolset!

This page contains some important information regarding how to set up and use PLINK. Individuals familiar with using command line programs can probably skip most of this page. Download PLINK is now available for free download. Below are links to ZIP files containing binaries compilied on various platforms as well as the C/C++ source code. Linux/Unix users should download the source code and compile (see notes below). These downloads also contain a version of gPLINK, an (optional) GUI for PLINK. Please see these pages for instructions on use of gPLINK. Remember This release is considered a stable release, although please remember that we cannot guarantee that it, just like most computer programs, does not contain bugs... Platform File Version Linux (x86_64) plink-1.07-x86_64.zip v1.07 Linux (i686) plink-1.07-i686.zip v1.07 MS-DOS plink-1.07-dos.zip v1.07 (to be posted later today, 30-Oct) Apple Mac (PPC) plink-1.07-mac.zip v1.07 (to be posted next week) Apple Mac (Intel) plink-1.07-mac-intel.zip v1.07 C/C++ source (.zip) plink-1.07-src.zip v1.07 One more thing... If you download PLINK please either join the very low-volume e-mail list (link from Introduction page) or drop an e-mail to plink AT chgr dot mgh dot harvard dot edu letting me know you've downloaded a copy. For old versions of PLINK please visit the archive. Debian users PLINK is available as a Debian package, see these notes. Note, the executable is named snplink in the Debian plink package. Development version source code You can download the very latest development source code in this ZIP file. This is really, strongly not recommended for most users. The code posted here could change on a daily basis and is not versioned. Development source code versions have a p suffix, meaning pre-release. For example, if the current release is 1.04, the next stable release will be 1.05 and the development code will be 1.05p. Note that 1.05 may differ from 1.05p and as noted before, from day-to-day the 1.05 development code may change in any case. The principle reason for including the source code here is to allow access for specific users to specific, new features. These features are described here. General installation notes The PLINK executable file should be placed in either the current working directory or somewhere in the command path. This means that typing plink or ./plink at the command line prompt will run PLINK, no matter which current directory you happen to be in. PLINK is a command line program -- clicking on an icon with the mouse will get you nowhere. Below, on this page, is a general overview of how to use the command line to run PLINK. The next sections give details about how to install PLINK on different platforms. Windows/MS-DOS notes Unzipping the downloaded ZIP file should reveal a single executable program plink.exe. The Windows/MS-DOS version of PLINK is also a command line program, and is run by typing plink {options...} not by clicking on the icon with the mouse. Open a DOS windows by selecting "Command Prompt" from the start menu, or entering "command" or "cmd" in the "Run..." option of the start menu. The folders c:\windows\ or c:\winnt\ are typically in the path, so these are good places to copy the file plink.exe to. You can copy the plink.exe file using Windows, as you would copy-and-paste any file (e.g. using the right-button menu or the keyboard shortcuts control-C (paste) and control-V (paste). Alternatively, if you know that you will only ever run PLINK on files in a single folder, then you can paste plink.exe into that folder, e.g. C:\work\genetics\. The disadvantage of this approach is that PLINK will not be available from the command line if you are in a folder other than this one. Once you have copied plink.exe to the correct location, you can test whether or not PLINK is available (i.e. in your command path) by simply typing plink at the command line. You should see something like the following message: Microsoft Windows XP [Version 5.1.2600] (C) Copyright 1985-2001 Microsoft Corp. C:\>plink @----------------------------------------------------------@ | PLINK! | v0.99l | 27/Jul/2006 | |----------------------------------------------------------| | (C) 2006 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| | http://pngu.mgh.harvard.edu/purcell/plink/ | @----------------------------------------------------------@ Web-based version check ( --noweb to skip ) Connecting to web... OK, v0.99l is current *** Pre-Release Testing Version *** Writing this text to log file [ plink.log ] Analysis started: Fri Jul 28 10:07:57 2006 Options in effect: ERROR: No file [ plink.ped ] exists. Do not worry about this error message -- normally you would specify your own PED/MAP file names to analyse (i.e. the default input filename is plink.ped). Please ask your system administrator for help if you do not understand this. HINT In MS-DOS, you can to increase the width of the window to avoid output lines wrapping around and being hard to read. To do this under Windows XP DOS: right click on the top title/menu bar of the window and select Properties / Layout / Window Size / Width -- increse the width value to a larger value (e.g. 120, or as large as possible without the window getting too big to fit on your screen!).

Anxiously Taking Off...

Source: http://upload.wikimedia.org/wikipedia/commons/6/64/Malaysia_Airlines_Boeing_777-200ER_9M-MRO_IST_2012-1-23.png

Finally, after 6.5 months, the first phase of my PhD is sort of taking off. I hope that this first phase will reach its final destination of a first year report which enables me to officially become a Cambridge PhD student, rather than the current probationary status. This post also serves as a tribute to all the passengers of MH370, the aircraft which also the last location where my cousin worked as the cabin crew. Despite not knowing him well when he was around because of our large age gap, I know David, my cousin, worked hard his whole life, and went through various struggles. He never gave up on life, on love. I wish I can learn this attribute of his.

I am nervous, and anxious too, especially after such a long hiatus on research due to my health, the travels, and the graduate conference (as much as I tried to deny the fact that I did put in much time and enjoyed doing it). Sometimes I dislike the fact that I could catch a cold too easily, and with the new addition to my medical history of acute sinusitis, my sinuses become infected twice this year alone. All these took time away from me trying to work hard because I sleep for days. Right now, I am worried I can't meet the par of passing my first year though I have another 3 months before the reality sets in. What if I have to go home because I can't complete year 1 and pass this probation? Everyone knows he/she has worked hard for a year, so it is natural passing first year isn't difficult. For me who spent most of my time sleeping and idling, it is as natural as them, only I'm at the other side of the fence. Working hard is not my forte. Yet, I know it takes hard work whether or not I'm good at it.

I saw this online when I was searching for the quote... "Don't be upset with the results you didn't get from the work you didn't do".

Source: http://www.savingadvice.com/articles/wp-content/uploads/2013/08/insecurity.jpg

I guess me browsing through the Wellcome Trust Sanger Institute is a cause of my anxiety. There is a group who is doing an awesome job with malaria. I saw their papers and found those interesting. Who am I to compare to them? All highly-skilled bioinformaticians and biologists; big brains gathering big data as a team of researchers. I need to overcome this insecurity I feel from within, really.

This is my behind-the-scene, nothing too bright or shiny, as how anyone would see a Cambridge graduate student should be. We all are still graduate students, just like anyone else in the world. We struggle too, and maybe, more than the rest of the world.

Literature Review

In the midst of searching for the light at the end of a dark tunnel, I begin to wonder how to do I wade out of the marshland of "Hows?". I know more reading, and more questioning, might help the process. And I wish for more shortcuts to understand the papers I'm reading as I form that big Q. It seems to me that everybody seems to have a relatively easy time to form the big research Q, minus me. When will I be able to form a proper big Q which is good enough to impress the MA?

Source: http://static2.quoteswave.com/wp-content/uploads/2012/01/The-big-question-is-whether-you.jpg

Everyone has his own method of literature review. Mine may not be the latest method. This is just what I know and most comfortable with. Let's return to MY way of systematic literature search:

1. I start with the journal which is directly related to my topic of interest.
2. Chronologically, I chose to start from the latest discoveries - some research paper with direct interests which seems pretty similar to my research group's methods of interest.
3. For more comprehensive understanding of the topic, I choose the latest review paper.
4. It is important to take note of the list of references of those papers I am reading.
5. More reading, and note taking.

This is a method I found published on the student support website of UCLan..

Source: https://www.uclan.ac.uk/students/study/library/literature_search_tips.php

I'd recommend the use of Mendeley desktop to aid the walk in the forest of references. So far I find using a reference manager very helpful and systematic. Others might have different recommendations.

The Fifth Month of PhD

In another seven months, I will either be deported back to Malaysia without completing a PhD, or successfully passed the benchmark of first year. I have three days before hitting the end of my fifth month here at Cambridge, and entering the sixth month of this caffeine-pumped, worries-filled life of mine.

Developing a proper research area and questions is something which has been bugging me since day one of my PhD. I know everyone is worried, especially the Man Above (MA). I do have some ideas forming at the back of my mind right now, but I'd have to test them out before talking to him. MA is a kind supervisor, but it is due to my own guilt of not doing enough that I find him fearsome. I guess I'd have to slowly work out that fear and guilt I feel within me when it comes to speaking to MA.

I'm still keen on doing forensics-related research which has connection with my team's main work on Molecular Evolutionary Genomic Analysis. It all has to do with my previous Masters research on DNA profiling. It is all possible, but I'd need to read more before presenting the baby to him. Let's just say I'm interested in the works on Kenneth K. Kidd for now...

Source: http://blog.illumina.com/img/dna_mag_300.jpg

Toolkit Story

Everyone needs a personalised toolkit in order to achieve their goals.

A surgeon needs his tools and team to ensure his patient can undergo a safe and successful operation under him.

Source: http://upload.wikimedia.org/wikipedia/commons/0/08/Surgeons_at_Work.jpg

An artist needs his brushes and paints and canvases to produce beautiful paintings.

Source: http://columbiametro.com/images/cache/cache_3/cache_d/cache_c/3dc8a408a597b5d093d73c57cc67ea3a.jpeg?ver=1400749198&aspectratio=1.5

A mountaineer needs reliable mountain gears to ensure he arrives at the top of a snowy mountain safely.

Source: http://www.mountainguides.com/photos/gear/backpack-tahoma.jpg

As for me, a PhD probationary kid, I need to achieve part of this network of computational biology.

Source: http://compbio.mit.edu/teaching.jpg

So, the first step is to understand what it is all about, and to find the right tools to start working on it. It seems to me that I am looking more into the area of computational genomics in the sense of biological anthropology these days, so there are a set of tools (packages or whatever one would call that) which I can pack in my imaginary backpack to get me going.

Source: http://www.compbio.cmu.edu/images/background.gif

Will I be able to form a proper research question by the end of my 6 months here? I have another month to ponder about this. While pondering, more packing to be done for the next chapter of my journey...

Source: https://cord-global.terradotta.com/_customtags/ct_Image.cfm?Image_ID=57

Writing Your First Year Report

I attended the course conducted by Dr. Geraint Wyn Story for GSLS (Graduate School of Life Sciences) PhD students to learn how to write my first year report. I know it is still a few months away before I start freaking out totally about it, but I guess it is better that I prepare myself right from the start rather than stressing myself out not knowing what I need to do when it is time to submit that very report which will determine if I stay or leave Cambridge. To be honest, I am freaking out already despite the fact that the first year report seems to be a very informal event in the division which I am in. Furthermore, the man above has been pushing me to produce results. I feel like a child who is asked to run when I am still learning how to crawl. Yes, the sense that I am stupid exists, and I feel very real about it, though I am more assured after attending the session that it is alright to feel how I feel.

One thing which is encouraged in developing our writing skills is to write regularly as a on-going process. A new concept (maybe not-so-new) was introduced -- "Writing to Prompts". This concept uses question or fragment of a sentence to stimulate the writing process. I do find it beneficial as it helps to focus our mind into writing something. Personally, I tend to break down the things I want to write into subtopics, and then explore the literature and read them accordingly, sometimes making notes based on sections of the same paper.

Another interesting idea is to do "Free Writing" of about 5-10 minutes with a suggested ideal frequency of 3 times a week. Writing without stopping for a duration of time on a certain topic indeed will help to free-up the writer who is bogged by the research and improve self-confidence. When we practised this concept, I came up with a short entry on "First Year Report Training".

One more concept before I end this post is the introduction of "Writing Groups" to act as a social activity plus an encouragement to help us write, and to make writing fun. Anyone would like to be my partner in crime for this?!

The usual culprits of a good report would the standard format, and everything else is rather dependent on the department. First year report should focus on introduction and future works with some prelim results and methods if there is any. A little about referencing was covered, and the importance of knowing who will be reading the first year report, and who are the examiners, plus the importance of appointing a secondary adviser. Gantt's chart is suggested to be a part of the first year report to give an idea of the audience what I plan to do.

This takes a bit of my time to digest it.

I'm ending this with something from PhD Comics. Cheers!

Source: http://www.phdcomics.com/comics/archive/phd030712s.gif

First Year Report Training

The day was gloomy when I woke up after the multiple alarms went off. It was a dread to try to wake up these days but I knew how important it is for me to connect with people studying Life Sciences and to know about first year report. The people in........***censored***........... It has been a lonely journey.

After a series of missing bus, getting lost and finally getting there to listen to Dr. Geraint talking and the PhD probationary students speaking of first years' worries, though more questions popped up but I'm assured that I'm not alone in my struggle to bear future responsibility as a Cambridge grad. Perhaps it doesn't take a super genius to get a PhD done here.

There's still some time left. Let's see how it goes.