Wednesday 27 August 2014

Budget, Scholarship and Happy Graduate Student

Yes, I know I need to do my work, but I can't help but to write this post.

In my previous post, I mentioned I am just a poor scholar here at Cambridge. I compared my currently scholarship with the Erasmus Mundus masters scholarship which I received for the past two years, which was a very handsome amount of money. I know this can't be compared. The payment system is different. I used to receive monthly scholarship allowance, plus mobility fund every start of 6-month term. I was pretty much able to spend when I needed to.

Source: http://i.telegraph.co.uk/multimedia/archive/01811/cash_1811300c.jpg
As for now, my scholarship installment comes thrice a year. It means I get 4 months worth of scholarship allowance in one-go. It gets dangerous when the mind is switched to "I have tonnes of cash to spend" thought. It took me about 6 months to psycho myself back to the mindset that I am not as poor as I think I am. If I budget properly, I can stretch every penny I have for food, entertainment, transport, travels, and SAVINGS.

I find this article on "Student MoneySaving Checklist" highly useful for those who need some ideas on how to stretch every penny we have. What I do is within the checklist of 50+ items of how to save as a student.

Source: http://www.studentuniverse.com/student-blog/wp-content/uploads/2012/10/budgetingpiggy.jpg
Yes, I do monthly compulsory savings. And no, I don't touch the money at all. That's my emergency cash in case I need to fly back to Malaysia at any point of my graduate studies. It is still not enough to fly back, but if I start touching it habitually it, it'll never be enough. I am using Llyods Bank, and the best thing is I could have three different accounts under the same name, so I started a compulsory savings account which the money from current account is auto-debited monthly. I also have a savings account for all the accommodation money I need to pay per term. My current account is almost always out of cash, with the lowest I got to was about £10 in it (end of the month kind of situation).

It's not easy to start budgeting, but once we get the feel of it, we'll be living a happier graduate student life!

P/S: I still do get to travel a bit with the limited budget I have...

I saw Giant's Causeway in Northern Ireland end of June 2014, thanks to the budgeting I made from the start of the year.

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



Wednesday 6 August 2014

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...


PlatformFileVersion
Linux (x86_64)plink-1.07-x86_64.zipv1.07
Linux (i686)plink-1.07-i686.zipv1.07
MS-DOSplink-1.07-dos.zipv1.07 (to be posted later today, 30-Oct)
Apple Mac (PPC)plink-1.07-mac.zipv1.07 (to be posted next week)
Apple Mac (Intel)plink-1.07-mac-intel.zipv1.07
C/C++ source (.zip)plink-1.07-src.zipv1.07

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!).  

Friday 1 August 2014

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.