Of history and blogs

For quite some time now, I've been trying to recall the blog I used in my sec school days. I used it pretty extensively... grumbling about school, confessing my love for chemistry, posting tons and tons of chemical structures that I created with ChemDraw. I couldn't recall the site anymore... but I did some googling work and finally found it today. 'Found' it. You can see this news article: http://www.moe.gov.sg/media/press/2005/pr20050909a.htm

My school won second place pfft. But I was part of the blog contributors who made it happen.... So I do am glad for that... but sadly... the site is long gone... and with it all my entries. I can barely remember what I wrote there, though I did remember that pretty much every entry was about chemistry. Esp the pharm chem option I was taking. Man. Those were the days. The days when I was still in love with chem. How did I end up in bio now? Pfft. Blame it on the JC days. *Sigh*. 

Sad that I can't look at my old posts again. Would have loved to keep a copy for old times sake. Been recalling the stuff we learnt in sch and did in labs. It's sad. I barely remember a single shit from uni days when it was just a few years back... but I remember so much stuff from sec sch when it's been a decade or longer. Why so? Cos it goes like this I guess. 

Lecture: Prof teaches about NCBI BLAST.
Me: What the heck. I freaking learnt that in SECONDARY SCHOOL.

Lecture: Basics of org chem... showing all the functional groups
Me: Scans through the list. Ahhhh I've read about them all in SECONDARY SCHOOL. Except for this one! ONE new item. Wow -.-''' *rolls eyes*

Lecture: Separation techniques - GC, HPLC, MS, NMR, UV VIS
Me: I learnt that in SECONDARY SCHOOL, JC (H2 and H3 chem?), and we're learning it again? And what, there's NOTHING NEW in these lecture notes? Are you kidding me? 

Lab prac: Gel casting
Me: Zzzzz are you trying to bore me to death? We freaking did that in SECONDARY SCHOOL. All the time. So many times. Ok at least we get to use EtBr here. 

Lab prac: Cell culture
Me: But... I was doing so much of it in my INTERNSHIP already.

I do remember some of the stuff that we did for the first time in uni... like SDS page and protein pull down assays... but so many things were repeats, or simple add ons to my sec sch knowledge that it's no wonder that I don't remember them at all. Boring, duplicated experiences. Gah.

I realised my 'first' blog is gone too. Myspace. I didn't migrate it. I hardly posted a thing there though so it's fine... Oh wells. 

I checked my very first entry here. I wrote that this is my 3rd blog. I guess the myspace would be the first, followed by moblog… and then this. Afterwards I had a gaming blog… then LJ… and now a wordpress. 

I’m reluctant to completely abandon this blog just for old times sake… but maybe… maybe it’s time. Either that or… this blog needs a serious face lift. I don’t know. Just looking at the tags I have and really… it’s been a long time. Gah. Chem spa? Lololol. Well this was made in j1 after all. Hahaha! Oh wells. I’m hardly using this anyway. No one visits this place anymore either I guess? And IMO bloodspot itself has become outdated. Ok LJ is dying but that’s a different matter. 

Oh wells. Started my wordpress projects today. Let’s see how they will turn out… *cough cough*

FYP, Convocation...

Its been so long since i posted here about school stuff...

Been slacking all along...

FYP ended successfully... despite me rushing non-stop for like two days at the end... things were really last minute... the friday before submission (mon 4pm DEADline), we were still carrying out experiments till really really late at night. With the data to be included in the written report...

At least the experiment worked out...

Things was really really drama at the end i tell you....

The last experiment we did was a pcr... after that we ran our products on a gel and took pics of the result...

Unfortunately... in my rush... i did notice that the files had a weird .1sc format... but i thought i could easily get some external program to open it...

HOWEVER... that was not the case... after trying all sorts of photo editing program... i FINALLY came upon bio-formats that is said to be able to open it... after downloading the program however... i was totally confused as it didnt seem to be doing anything at all. further searching and i finally understood that its actually a plugin for the software ImageJ....

Things was quite frustrating at the end… i was clearly behind in my report writing, and got really frustrated when my buddy kept asking me for help on the simplest of all things. Made me really really frustrated as i felt i was constantly spoon-feeding her. And its not like we're a team or anything, sure we are friends, working on similar things for our FYP, but everything is graded individually… I'm not obliged to help her and the thing is that it doesn’t feel like a fair exchange of ideas. i felt like i was the only one bringing things to the table while she was just feeding off me. It really made me doubt if she even had the ability to do anything on her own at all, though she put me wrong as she too, managed to find the bio-format and imagej software. So what was she doing all along then? Must she ask me to send her EVERY SINGLE THING? Every website, every small program i use… yeah it was really frustrating.

But its all over now. Report was really last minute tho, wrote for almost 3 days and only finished on the morning that it was due… started printing out the report at like 11+am when i had to submit it by 4pm… its like… I'd just kill myself if anything went wrong with the printer or something :X

Either way… its all over now.

Ah and poster presentation. Was crap. As in… i didn’t get a single examiner. Stood there for 2 days and no examiner. meh. it really made me sad… i was so ready to present my poster which i put a lot a lot of effort into… made the pictures look really nice and such… i wasn’t the only one who didn’t get an examiner tho...

My mentor wanted to keep my poster… so all i've left are memories and pictures. oh and the soft copy, of course. sighs… i still can't help but think about my pretty molecule alignment picture… well all credits to pymol of course… but then again many others, my friend included, didn’t know how to get a high res picture out of pymol so….

And yes… convocation is over too. Nothing much really, just going on stage to get the folder, getting the transcript with my horrible results at the back of the hall… haiz.

Pics some other day maybe… :X yes i am a procrastinator. 3 months to post about my fyp? lol!

Almost there...

So I'm finally done with my poster design... barring any mistakes or changes that my mentor wants... and pending changes from my dad and my sis (like i asked them to give comments on the color scheme and stuff, the science and the actual content they don't understand ><)
well my sis is way better than art then i am (actually, my dad too), so i asked her to give some comments on my poster yesterday... i was telling her that i tried to make my poster as less wordy as possible... but she was like 'huh? u call this not wordy?' gah! It can't be helped that the intro, methods, objectives, and conclusions all HAVE to be in words right? tch! Already i've put like huge pictures and graphs to make things as pleasing as possible - while still retaining its 'scientific-ness'...

I decided to do things differently this time round... following in part my experience at SSEF when i was in junior college. I cut out whole portions of the report from the poster, and didn’t present a lot of the obtained data. I don't want my poster to be a case of too cramped, too much info, and too confusing... i felt that last time i didn’t win at the SSEF cos apart from that fact that I'm not THAT good a presenter (I'm not the very lively, talkative kind), there was also too much info in the poster/report. If I'd cut out the last part of the results entirely and focused on something else instead, the results could have been very different. Regrets regrets sighz... you live and you learn... what else can we do?

So yeah, i cut out the entire lab work part (which wasn’t much to begin with anyway) and only focused on the bioinformatics. I also didn’t attempt to squeeze results for everything for both genes in... either or, not both of them. No tables of long lists of numbers either - i changed it into a graph instead. BLAH that stupid graph took me SOOOO LONG to get done! The new office layout was really confusing for me - cos the last time i work extensively with excel was... like... 5 years ago or something... using the older version of excel. (plus i wasn’t on mac yet). Than direct copying and pasting the graph to powerpoint didn’t work. I was really really pissed with MSoffice then... like WTF on earth are you doing! The graph copies over alright, but it changes the freaking style and everything that I'd painstakenly arranged in excel! and i can't change the style back in powerpoint! Then after googling i found out that i could use the paste special thing or some sort, but it only worked in another ppt doc, not the one with my poster... in the end i took the nice looking copy pasted in the other ppt, saved it as a picture, than imported the picture to my poster. zzzzzzz! so troublesome! The resolution should turn out alright... i hope ><

ah my mentor wanted pictures of bleached corals too... i took like over 5 hours to search for copyright free etcetc images that i can safely use on my poster... finally found several on flickr (i don't use flickr so it too me a while to remember which site it was that had the creative commons license thing, at 1st i went to gettyimages but like nothing is free?) and picked two out of the lot. Next problem was that i didn’t know what species of corals they were... searched around for a bit but only managed to identify one of the two... gave up in the end ><

and than there was the stupid guide tree. oh gosh how many DAYS have i spend on the phylogenetic trees in total? i really lost count! From that time when writing the report to now the poster...! At the beginning i skimmed around for something that can open/plot dnd files... didn’t find anything that worked, so i skimped on the work by screencapping from the clustalw2 website. Than my mentor suggested that we put in bootstrap values... (that was like, a few days before the report was due). So i started google to find out what ARE bootstrap values... (very last minute, i know). Turns out that i had to use clustalx to generate those so... thankfully i downloaded that a while back. So it took me a while to tinker around with that program... and hohoho! It generates the raw files, but you have to use something else to open the raw files. BRAVO! After a lot of fail attempts (some required you to compile the program yourself, but somehow when i try to compile the files it just WONT WORK!, others were like powerpc programs or something which apple withdrew support for in Lion...) i finally got njplot to work. BUT that stupid program could only generate trees that were A4 sized. So things ended up being really cramped...! I ended up having to draw a sub tree for one of my genes zzzzzzz. And that's the big problem too... for my poster i needed the tree to be more like in a landscape kind of orientation (otherwise no space!) which the program can't get me. I ended up resizing the window and screencapping AGAIN. But that's bad because you end up with the tree on a white background. I want the background to be transparent.... -.-''' So i took a million years with photoshop and stuff, in the end i had to trace out the tree in photoshop and type out all the species names separately in powerpoint.... sighz.

So yeah... hopefully everything is alright with the poster now!

Poster

Blah... it just started raining HEAVILY. like real heavily. i guess i'll go home late again today.

So next tuesdays n wedn is poster day... discussed with my mentor just now abt the poster and i have quite a bit of work to do. been spending the entire afternoon looking for a nice, copyright free (or watever u call it) pic of bleached corals to use in my poster. Found two nice pics to use in flickr... which I'm free to use as long as i credit the photogs.. hopefully i understood that creative commons thing right that is ><

blah........ that's how I'm feeling right now ><

 

Really the last last bit left of school to go… report was handed up already last week (after a long struggle) so all that's left is this poster thing.

Last bit to go...

busy busy busy...

yeah yeah i know… i've finally broken my 1 post a week promise… but i've got my FYP report to do so yeah… gotta go!

Lab

So i finally started on lab work stuff last week. Like last Tuesday? Started off with extracting DNA with another fyp student, so that we can sort of get to know the procedures and know where everything is in the lab. prior to that i've not even SEEN the labs bravo.

Following the other fyp student around totally reminded me of my time at ibn when i followed fan around. heck, maybe i reminiscent about the past a bit too much for my own good… but i can't help it, that's just the way i am :X

The way this lab works is totally different from the individual research group style in ibn. There its one group one lab, and in my previous lab our relations between group members was pretty good so… there wasn’t any hard and fast rule like exactly which part of the bench belongs to who… pipettes i just use whatever's on the rack - most of the time there's no name written on it anyway…

Here, its more like an individual thing? like you use your own pipettes and stick strictly to your own space. fyp students in sbs were each rented a set of pipettes… but somehow there was communication disparities… when we emailed the prof to ask, we were told that ppl working in that lab didn’t have to attend the safety briefing (and hence no pipettes)… but other fyp students from my course DID go for the briefings and were given pipettes -.-''' zzzzzzzzzzzzzzzzzzzzzzzzzzz a little zzzzz up to me but yeah… at least we aren't gonna do much lab work… and we're just using my mentor's stuff. and work space. things are kinda weird in here… like the lab ppl were asking why are there suddenly 2 more students in the lab when our mentors did inform them long ago that we will be in the labs. admin stuff tsk. always so troublesome...

working in the lab made me feel… alive though… like i finally have a motive, an end in mind… what to do etc. made me realize that as much as i love doing stuff (games, surfing the web, writing blog entries etc etc etc) on my comp, working wise, i prefer lab work to… bioinfo stuff. granted when u do lab work u still have loads of reading and writing to do, but at least… somehow… the lab work in an anchor? keeps me more focused or something… my place is in the lab… not the office… i feel more at home in the labs.

So we spent the better part of last Friday preparing the reagents… and after that we discussed about the intro.

And yesterday… ah.. my mentor has a habit of coming really late. We were supposed to meet at like 10am, but he turns up after 30mins or so later, and than checks his emails and other stuff on his comp… and we headed off for the labs like… maybe at 11 or so? i actually don't mind the time i have in the morning to use my comp and stuff… its just that starting at 11am? we worked all the way till 4pm. Lunch at 4pm… bravo… my stomach died a bit halfway through :X

So we'll be continuing with the 2nd part of the experiment today. At 2pm he says… i think we'll take till… 7-8pm? since we'll probably start closer to 3 than 2pm. Not the 1st time we ended at 8 though, just last Friday our report discussion took us all the way till 8pm.

ABout the intro that i showed my mentor last Friday… blah… it wasn’t the best piece of work i've ever written… its all broken up in bits of disjointed text… quite a horrible piece of work really. in contrast, my friend has got the intro nicely written up already. Only that i kind of fainted when i saw the 1st part of her intro. It was a totally non-scientific way of writing… in my mind i was like what the hell are you doing? delete that whole 1st para kind of thing :S sighs… the differences between the two of us. i think i kind of over reacted at 1st tho and i was glad i didn’t say anything else i would have been totally rude. my mentor did ask her to change away that part tho so all's well.

I shd care more about my own pathetic piece of writing than criticizing the work of other's. At least they have a proper, flowing introduction already, which is a lot more than what i can say for myself :X

sighz, I'm still the same as before. unable to find the mood to write and only able to do last minute work. no pressure, no work. sighs. At least i don't play games or watch videos in the office, but i do end up spending time to blog instead :X

managed to get mendeley to cite stuff the way my sch wants for my report… sighs. really feeling like a zombie today… and i already slept 7 hours last night… some how its still not enough? sighz.

kk, back to my pathetic intro.

sch and such

hmm so i haven posted here in a while...

in truth tons of things i want to blog about...

but no time...

so this shall just be a short post...

 

schools the same, 51 days till my report is due… and still getting no where with nothing. no good...

 

going out cycling with my friends tmr morning! roots, finally get to see ash after EONS. can't wait!

 

WX invited us to go dinner + clubbing next wed… nor been clubbing before, not sure if i'll go… cos its ladies night so yeah… meh…

Days long forgotten

That's the water bottle I'm using now… yes, the water bottle they gave us during JC1 orientation… that's like 6 years ago… seems so far and so distant. My sis sent me a youtube video of the RI(JC) IHC opening video for last year yesterday… and i started watching the rest of the related videos… amazingly i found the ultra lame video they showed us during orientation… the one about the different houses being greek mythology gods/goddesses and being banished to Z'kardia… got tons of dislikes and flames on youtube though… LOL.

But its kind of nostalgic… watching the orientation dance of the other batches and all (couldn’t find any for my batch tho, sad). Seems like in the recent years they started making really nice MVs of the orientation dances. And than there's the sun dance that's passed from one batch of OGLs to the next… i really liked watching that dance during my orientation… the dance is cute, hilarious… and really simple to follow - i did it once during the orientation… when the whole OG stayed in sch till like midnight to dance and have fun. I told myself during the orientation - when we just started doing the batch dance - that i was gonna do it properly and enjoy myself… and i did have a good time. Don't regret it, cos that was like the last time I'm ever gonna do something like that again… mass dance and all… didn’t go for uni orientation… and don't think i'll ever do something like this next time… Yeah… the batch dance… its really hard! Rather lengthy and all different moves… different moves for the girls and the boys… and they don't constantly repeat moves that kind of thing… I was talking to someone from another JC that time (when i was in J1 and we just finished orientation, it during during CNY when we were visiting my parent's sec sch friends)… and she was like 'what? you all only have one dance? so lousy! and how come you all can't remember the dance? we have like 4 or 5 (i can't remember how many) dances and everyone can remember all the moves!' Than she showed me her orientation booklet and i understood why… One dance consist of just 10 (or so) short moves (things like box step = 1 move) and the 10 moves are repeated over and over again throughout the duration of the music/song. Of course everyone can remember them. Ours? Some ridiculously hard dance (really, a dance!) with all sorts of different moves for the entire duration of the 4min? song that's impossible for normal people like myself to remember the steps to… without having my OGL there to demonstrate that is. Its like i absolutely can't remember what's coming next kind of thing. But still, the dance was really fun… I really enjoyed myself during the orientation...

Perhaps you can say that it's really stupid of my sch… to have such a difficult dance that like no one can remember… and that its better to have just a very simple dance that everyone can groove to… perhaps…? Well its not that my batch dance was difficult or anything… its just that we can't remember the steps and need someone to show/remind us - something which my lovely OGL did most of the time. We CAN do the steps, but we CAN'T remember when to do what step :X does that even mean anything? haha… still… we had fun and that was what mattered most. Granted, there were many ppl who absolutely hated it, but its really how you want to look at things… doesn’t matter whether the dance is easy or hard or stupid… as long as you tell yourself 'I'm going to enjoy this', you will.

 

Anyway back to my water bottle… started using it either last year or last last year after all my previous water bottles ended up in failure… either they got moldy or they leaked etc etc… Really like the aluminum water bottles… especially this one that's in my favorite shade of blue… XD Especially when you fill it up with cold water from the water coolers… The whole bottle will frost up almost instantly and ah… the nice cool 'ice pack'! And after leaving the bottle in the cold lecture theater (or anywhere cold) for a while, the water instead is nice and cold too XD Love it! Only thing is that every time it falls… Its gets dents… and with the stupid lose side pocket of my bag, that happens quite a lot… :X So much so that i've just taken to securing the bottle with a carabiner to my bag strap… o.o

 

Okays… I should get back to work now!

Mendeley!

Heh, i've been posting quite some bit recently, many of them with more photos than words. Well, I'm certainly glad that i managed to keep with my 'at least one post a week' promise… though it doesn’t exactly help with my writing skills since i've not been doing much of a proper writing recently. One thing for sure, is that MarsEdit really helps a lot in encouraging me to post. I can see at a glance which blog i've been neglecting etc… being able to see when my previous posts was motivates me to post things. And i don't have to go through the trouble of opening up my different blogsites. And ah, the ease of posting photos…. its much easier to post just a short entry with some text and loads of pictures. In a way its cheating, since it defeats the purpose of me wanting to practice my writing and typing skills… but it's not always that i have the time and mood to type long entires… nor the material/topic to talk about… so i guess all's good.

FYP is getting pretty hectic. We are, indeed running rather behind time… however, since i've decided to take time off to blog, (spent quite some time on blog entires in my other blog already)… I might as well spend some time to talk about this wonderful program i've found…

So, some time back, i was thinking to myself that i HAVE to start organizing and filing my small but steadily increasing collection of research papers before things get way too messy. The big problem with research papers for me is that, organizing them is such an awful chore… worst still, i don't even know how to organize them. 1st: the naming problem. When you fetch the pdf from the database, they either call the pdf by 1) some weird jumble of letters and numbers 2) some generic thing like 'science' or 'fulltext' 3) sometimes if they are nice, they'll call it something relevant, like the author or something… Most of the time though, i have to rename the file, and it always leaves up struggling to find a way to name my files WHILE allowing me to know what the article is about. Some ppl go by the arthur names and year, but that really doesn’t help me understand what the article is about… since I'm not familiar with the researchers in the field and all… Paper title? Most of the time the titles are very lengthy…!

After wasting loads of time searching and trying various apps (i was even seriously contemplating using iTunes to organize my files!), I finally found Mendeley. Actually, quite a lot of reviews have mentioned it, but i was reluctant to take it up at the beginning because it can sync the documents online… which ironically is a feature i found very useful later on.

Mendeley is an app like no other… None of the other programs i saw or tried even comes close… There's endnote, there's many other pdf file managers, there's Papers - this expensive 80 dollar app that sounds really great in functionality… but ah, the price tag...

What can Mendeley do and just why do i like it so much? Let me try and explain one by one.

First of all, its FREE. Yes… FREE! Well the free account includes 1GB of online storage, 500mb for your personal use and 500mb for sharing (more on that later). Well its not a lot, but than research papers usually don't take up THAT much space per paper… and if you have too many papers, that means u just can't sync them all online, you can still use it normally on your desktop, no problem. You can also pay for more storage space of course.

2) It runs on mac. And windows. And iPhone/iPad. Cool! That means that you can sync your collection of papers over your various computers, and i can even read the papers on my phone if i want to. Doesn’t let you do much else on the mobile apps but… i don't really need to do much else.

3) It manages the pdfs really really well. There's a lot of factors that make me feel that way… like:

Watch Folder - You can select folders that you want Mendeley to watch. That means that any pdfs you dump into that folder will be automatically added into Mendeley. Convenient much? Now i can simply save the pdf in my folder labelled 'papers' (oh how informative) and be done with it.

It scans the pdf for data - Mendeley doesn’t just rely on the pdf's metadata, it also SCANS the pdf file and will try to pick up details such as the DOI, title etc etc… It will also automatically check out their own database as well as google scholar to try and find any missing details… if in doubt, the program will ask you to check the data - you may have to put in the title manually (well, just copy and paste from the pdf) and ask it to do a web search… well if all else fails… there's always the manual input option.

It is a pdf reader on its own - Now that all your pdfs are nicely organized, you know which file is which… its time to do the actually reading. Wonderful news: Mendeley has a built in pdf reader, and lets you do things like annotations, highlighting, writing notes etc… and with the tabbed browsing, i find it much neater than preview. I also don't have to switch between finder and preview to call up another pdf file - i get it all done in one app.

Folders, smart folders - The usual folders allows you to group your papers. There's also a favorite button for marking really good/useful papers.

4) It can also manage citations and bibliographies. It can plug in to msoft word, open office etc… even has a nifty little shortcut key for adding citations etc in MS word. Neat.

 

I've tried endnote too, even attended a short course on it… but it was precisely during the course that made me aware of Mendeley's advantage over Endnote. (The librarian did mention mendeley at the start too, makes me wonder why they don't offer courses on how to use mendeley instead… but than again, mendeley is really easy to use… wait, endnote is really easy to use too, i didn’t quite need that course actually :S)

While endnote works really great as a citation tool, it fails so much in terms of pdf handling capabilities when compared to mendeley.

Endnote cannot scan the pdf. So if the metadata of the pdf fails, the whole pdf entry fails and you have to manually edit it. Sure, endnote is able to search many online databases, but it cannot merge entries. So i'll still have to manually key in the data for the pdf file, or i have to manually attach my pdf file to the online entry. Either way, its troublesome.

Mendeley is working to have more sites include a button to import the citation directly to the program, and they also have a little bookmark that lets you do that… but for me, I'd want to read the paper rather than site directly… i want a copy of the paper… so i pretty much add my mendeley entries only using pdfs. Same goes to endnote… only that mass importing of all my pdfs doesn’t work very well since quite a number of the files don't have proper metadata. It doesn’t have a watch feature either so i'd have to manually add in the pdf files… and if the pdf doesn’t have metadata, I'd still have to copy the title over and do a web search. So it quickly became such that i had to search the web database every time i want to cite the new article i just read (while simply writing down and organizing my background information in MS word)… which is quite a chore.

Endnote doesn’t have a built in pdf browser. AND because of its limitations in handling pdf file based citation entry additions, I'd rather use the web search to get my citations quicker. That means that it's not managing my pdf files at all (even having to file the right pdf file to attach to the right citation entry would in itself, be a challenge!).

So while endnote is a good citation tool… I'm simply going to stick with mendeley for my citation needs. It seems to do the job just as well anyway, and coupled with the easy library management, i'd say that it does it even better.

Things like scanning of pdfs is something that all other free/cheap pdf managers does not have. Oh yes, the scanning of the pdfs means that you can search within pdfs. Like you recall something that you read somewhere and want to call out the pdf, but that something you remember isn't in the title or even the abstract… mendeley's search function will be able to find it for you.

 

Overall, the program looks really neat, and has all the features i need. Oh there's even addition features that i don't need at the moment, like groups and file sharing. Its like a social network on its own, allowing you to create groups and share papers with other researchers. It'll be useful if say your research group are all using mendeley for example. But right now its just me by my lonesome self so yeah...

If you're looking for something to organize your papers, I'd say Mendeley is your one and only choice.

Happy Valentines Day!

Happy Valentines Day!

 

Today wasn’t such a good day at all for me… started off with a sore throat, which became a flu + fever...

feeling much better now though, thankfully. Almost done with my protein 1 blastn so… that's good news i guess.

 

Saw this being sold in the pushcart stall in ssh yesterday… and just had to buy it… heart-shaped one for my sis, apple for me.

opps… sorry for the photo spam… but $2.50 each for a pretty, color changing light device, with batteries included… i just couldn't resist… well i was feeling really frustrated with the blast work so yeah, retail therapy? lol.

Scary!

Doing swiss model now…

i have to submit the sequence to the site and after that they will send me an email when its done… since i got like 50++ sequences for my protein 1… now its like…. (i did quite a few of them already too, mind you)

SSCARYYYY!!!! Just of sheer volume of emails is overwhelming! I gotta go to each of the report and dl the pdf and pdb files… and copy n paste the info out...

 

And than i have protein 2 with 70+++ sequences to do clustal and swiss model with :S

 

Its not a hard job, but its tedious… exceedingly tedious, and very time consuming… just like how adding stuff to HS db was also a very tedious job. Its just that i have tons of other things to do like lit reviews, writing etc etc...

 

one step at a time… one email at a time...

Curiosities of Biological Nomenclature

Working on my FYP and blasting thru that various taxa… i came across a hit from the organism Botryotinia fuckeliana. Sounds like a swear word much? Well, there are a lot more weird names in bio… as this website shows...

Curiosities of Biological Nomenclature

EndNote

Whee. Just finished attending the endnote course. Most of the stuff I figured out on my own already, but I did learn some new stuff - like I have to change the endnote format to plain text when I'm done with my report - a stage which I'm still a bit far away from...
The instructor was very nice and energetic... And the classrooms were omg pretty! Nice seats, nice aircon... High tech screens... And they even provided sweets and some refreshments for us to have during break. And on top of learning abt how to export citations from various websites to endnote, I also managed to find a couple of papers... Some looks really promising too. I.e. having the info I want and need.

Glad I attended the course - tho it did get a bit draggy at times. Like there was this Angmo who ask the weirdest of all qns, like what is the use of creating groups in endnote... -.-" to manage ur references la baka! If u do, or if u start doing research u'll know just how messy all those refs can get...

K, I'll probably dabao subway to eat in the office once more.

Things I should do...

Decided not to go to school tmr… and this time round i HAVE to do work at home rather than just slack all over the place. At least i did progress by doing some blasts today… I'll try and get as much of the blast of of the way as i can before i go to bed...

Hmm lets see… i think i'm almost done with my structure research on protein 1...

So i've  got to continue reading up on 2nd protein… which is seriously complicated (all my previous attempts have ended up in failures)...

Still got to read up more on why i'm working on protein 1… and i have to do that for protein 2 as well… and than i have to read up on structure of protein two…

And finish up the blast for protein 2… and since i've gotten so many hits for protein 2, i should start on the clustalw asap else i'll die later or something… it’s a great thing there are so many hits for it… but that also mean more work when it comes to analyzing the results later… Its totally unlike the 1st protein where there aren't many hits… (even than, somehow i still had more than belinda… which is weird)… now i have so many hits that its crazy… there'll be like 4 or 5 hits with similarly high sequence coverage and a superb score… i'll still pick one only though… else it'll be way too many to work on… So many hits that its really crazy…! Crazily happy and crazily worried… if you know what i mean. I Should more my white board from above my bed to my book shelf. I should write out the stuff i need to do and leave it where its really obvious so i get reminded to do my work and all.

List:

1) Consolidate findings on structure of protein 1, write it out nicely

2) Consolidate findings on why i'm using protein 1 as a marker

3) Find out about protein 2 structure

4) Find out about protein 2 general info

5) Find out about protein 2 - why it’s a good marker

6) Finish blast for protein 2, and do a meta clustalw and clustalx

7) Finish up annotations for protein 1 clustal -> almost done

8) Start on clustalw for protein 2

9) Organise all the research papers i've gathered

10) Organise all the useful information i've hastily dumped in a word doc

Yes… i'm working on bioinformatics and its undoubtedly more relaxing than those lab work… but like 3 weeks of slacking off is really bad… if we can't keep to the schedule we won't be able to order the primers in time for us to do the pcr… which i really want to...

 

ok, back to blast!

FYP and EndNote...

Downloaded Endnote and configured Endnote a while back… Decided to get started with it and organize my references that i'm reading (and will most likely use). Might as well get things starts ASAP… its not like i'd have much time anyway. 3 weeks out of 14 is already gone… time flies!

Didn’t get much things done this week… still have not finished my blast on the 2nd protein and i've got tons of reading up to do.

Was quite happy on friday though. Did a ClustalX and saw that all the important features of the protein were conserved across ALL species… really amazing! Its like… wow, so this is for real kind of feeling.

I signed up for a EndNote course the following monday… actually wanted to get at the start of the sem but i forgot to sign up… forgotten that belinda actually went in like year 2 or something already… i was too lazy to go that time :S Didn’t realize that there was one specially for mac users but… is there that much diff? Thanks to belinda i managed to change the citation format properly and like… now i don't need to go for that course anymore… kinda figured everything i need out already :S. Opps. Maybe i'll end up erm… skipping it? Eepps… but i signed up for it already… with my matric number too… oh wells… i should just go for it… hope i can wake up for it in the 1st place :S

To Do List...

Things to do by 3pm tmr:

1) Meta clustal -> done!

2) Individual Pairinings clustalw -> done!

3) Literature review on why i'm working on protein 1 --> papers i'm looking for have remained elusive through days of searching… finally getting somewhere now… i hope.

4) find out structure etc of protein 1 -> not done

5) find out about protein 2 --> in progress... headache… this guy is such a mammoth, complicated protein!

6) Do blast for protein 2 --> started on it… well i don't have to finish this by tmr though.

 

need to get no. 3-5 done tmr though… since we'll be discussing about it again tmr.

Happy Chinese New Year!

Happy New Year Everyone!

恭喜发财！新年快樂！万事如意！

Here's wishing everyone a good year ahead!

Well… for the lack of CNY related photos… my sis took this with my phone just now

The past few days were kind of torturous… considering that i really really suck at packing, and i really hate all the dust… blah :( but well… since my relatives came over for the reunion dinner just now… it really forces you to pack the house nicely and all. Dinner was quite fun, played bridge with my cousins… and mum cooked way too much food as usual. Was supposed to be the yearly BBQ thing, but after the heavy thunderstorm on Sat, we decided to just cook everything at home and forget about the BBQ - a wise choice indeed cos it rained on and on. The year of the water dragon indeed.

My feet/heels are really hurting now…! From all that standing up i guess… even though it wasn’t really THAT much. Used my right and my right arm only to clean all the glass panels/mirrors… my right arm was pretty dead last night/this morning, and i guess it'll be worst tmr since i wiped some more this morning… oh wells. I did manage to meet up with wx, sandra and michie for lunch yesterday… just in time before wx gets her double eyelid + lasik surgery and b4 sandra goes back to austria for graduate med sch… cool yeah? wx's going to graduate law ssh in the US too… whereas i'm… still completely clueless about my future… and to think that i'll graduate in a few months OMG…. right now i'm just… i just wanna do my FYP and do it as best as i can...

FYP… total of 14 weeks only… 2 weeks already gone, entering the 3rd week… my work is a bit more troublesome than belinda cos the proteins i'm working on are… a bit more troublesome… like the ones i'm working on aren't that good and i had to change protein once… hope the 2nd protein tat was picked will go alright… but i really can't tell till i do more BLASTs… right now i've got to pick 1 out of the 3 possible candidates i've got so… unlike belinda who's already gotten a gene all set and ready to go, i've got a little bit more work to do.

Met with my mentor(s) for a discussion on friday… we talked for quite long, like 3.5-4 hours or so? I've got really a huge bunch of work to do… its like he gave us more work to complete in one week than wat we had for the whole of the previous 2 weeks… i guess that's hope things will go. It'll just get harder and less slack as time goes… i'll have to do a lot of literature reviews and i've got a thesis to write after all. Hopefully the bioinformatics part goes smoothy so that we can do the PCR too.

Since i've to check if my gene is alright and  discuss with my mentor on wedn if anything goes wrong… i've got quite a lot of stuff to do b4 wedn… sighs… not easy indeed. Its not like he's forcing us to do anything, but if i don't get things checked by wedn i'll lag behind belinda, which is no good… things are just gonna pile up and snowball if i don't get it done quickly.

 

Still, i'm taking some time off to enjoy myself a bit… hastily put up this banner on banned story just now. I want to install photoshop on my comp (on that dad has bought it), but i've got to clear my hard disk 1st… the installation of the bundle of software will take like 7GB of space… but now i've only got a pathetic 15 GB free. No good at all…. blah… its an irony cos i wanted to photoshop some of the pics that's why they are still on my comp, but i don't have the space to install photoshop so……. ZZZZZZZ

ok… here's the banner

my friend was saying the characters look really bad… oh wells, i was just picking some red stuff that has as much CNY feel to it as possible so it ended up like this… yeah...

okays… Wishing everyone a Good Year ahead! Night night!

Having a BLAST of a time

Having a BLAST of a time in school now… BLAST, stands for Basic Local Alignment Search Tool in case you are wondering. Doing Blastp now… and the site is taking quite long to process my queries… at least 2mins per search :S

So while the site is slowly searching, i do stuff like read up on the different taxa on wikipedia… or read up for the report writing and mini presentation on friday… or read the straits times… or read live journal… or write on my blog etc etc...

Came across this pretty photo on wiki...

pretty much? looks like some flower or coral or whatever? wrong! how about this...

 

any idea what it is?

well it’s the Strongylocentrotus purpuratus… or purple sea urchin!

 

Doesn’t look too much like a sea urchin does it? and its really pretty!

 

Gonna try and finish up as much of the  blast for this 1st protein as i can today… belinda's almost done with her's already… but cos i had to change protein so i'm a little behind...

ok, that's all i have to post abt BLAST…

School school school

Ok, let me post a bit about school and update you on what happened since… last december?

FYP started on wedn… was supposed to meet my sup on mon but he just came back from france and decided to push the meeting back to wedn… so far so good with the work. Nothing hard for now, and my sups are really nice. I'll need to do a bunch of reading up though… still kinda lost as to how the project will proceed later on. In a sense i do miss doing lab work… but doing this computer work isn't too bad either. I get to have things nice and slack… at least for now. My mentor wants us to make a short presentation on our protein next friday. I'm all for it… really really need the presentation practice… i'll probably be presenting stuff on a casual and weekly basis from now on. Yes i hate presentations, but that's partly because i've gone sooo rusty since the days in IBN or sec ssh when i made presentations really frequently. I would like to get my presentation skills back… so i'm really glad for the mini presentations my sup is making us do. Things seems pretty slack now too, he doesn’t expect us to work fast and stuff… but i do want to get things done faster, cos i'm such a great procrastinator and slacker… like i wanted to do work this weekend but what have i done? i slept the morning away, slacked in the afternoon, and got dragged out with my parents in the evening. Tmr? (or rather today) my parents are dragging me out for breakfast with relatives… -.-'''

Don't have the access card to the office… which is a bit troublesome… but its so much better for me to go to sch rather than stay home cos… i'd actually get work done in school… and fast… and slack a lot lesser than at home. i should probably get to school on monday...

 

CNY is coming and its coming really really fast…. relatives coming over for bbq on CNY eve again… that means that i have to pack my room… which is in a terrible mess! my worksheets and notes from last sem are stacked randomly on the table (thankfully i've gone as paperless as possible! only printed out my biz law stuff cos its open book exam) my shelves are super duper dusty… etc etc… sighs….

ok some photo spam...

Nanyang audi… my classmates where remarking abt how it’s the last time we'll be in that place for exams so yeah… at least…. last time for our degree...

this is taken from the front of nanyang audi… hall A… i was here for some… some core paper which i happily forgot what...

after my biz law paper… my small table is in wonderful condition…

from the back of the nanyang audi, where i was seated for biz law… my last paper!

the 1st time i've been in nanyang audi was for exams… other than that… i've only been in there for open hse… :S (either showing my juniors are or helping out at the booth)

its cute how they plaster the glass doors/walls so that ppl can't do funny stuff like wave placards with answers for their friends taking the papers… or something.

Ah… evidence of my passage through ntu… you know they always have the string to let you tie the answer booklets together if you use more than 1 answer booklet… i took the string and tied it to my pencil case… resulting in the above childish mess… so far i don't recall using a second answer booklet before… each booklet is thick enough… and we've had had a lot of mcq only exams :S (even than they still gave us a string, hurrah for my collection)

Towards the end i have having trouble tying the string onto the pencil case though… the zipper was choke full of strings already… but it’s the end now….

The night scene at the bus stop nearest to SBS

the night scene is quite pretty… the majestic trees standing still in the dark and quiet night… but its really quite dark, and iPhone (3gs at that) camera kinda sucks...

 

 

Ah this… was walking home together with my sis like… last week? or smthing… it was like… ard 11pm? Went to the market to buy the fresh milk that my mum has been bugging us to buy… my sis wanted to get ice cream from macs but there was a long queue… and while walking back home we saw the pretty moon… full/almost full moon… looks really pretty with all the clouds in the sky. noob phone cameras certainly can't do the majestic view of the moon justice.

The way the moonlight lights up the clouds in the surrounding is very pretty. Even with the cloudy sky, the bright moon can still be seen clearly. We stood there like idiots gapping at the moon for a while...

doesn’t help when the surroundings looks so quiet and peaceful...

in the end, we decided to get ice cream from the 7-11 opposite my house… and we happily sat at the playground/exercise area outside and ate… while enjoying the pretty night scene...

 

 

 

Ok… shall end off this post with the dragon statue? made from flowers i saw at orchard road earlier today…

as you can see (but may or may not know), its located outside the mandarin gallery…

 

okay, that's all for now… i shd get to sleep… gotta wake up at 8+ tmr… i bet i won't be able to wake up on time and i'll get another scolding from my parents… oh wells.

till next time!

WHEE! School's out, FYP's in

Hohoho. i'm back. yes. loads of updates coming up next, hang on tight. Ok... i'mm try and be more organised and split things into a few posts.... if that helps anything...

SCHOOL

ok, only school stuff in this post.

I stopped myself from posting as exams drew nearer. But its all over now... exams was ok.... that's all i ever say abt them isnt it? Well, i'm quite worried about muscles and omics... esp omics. All that i studied seemed to have gone out of my head. It was a fairly easy paper, but i could remember enough for the essay/short answer qns. Plus the mcqs were multi answer.... no good :(. Mol evo... the mcqs were tricky... and the essays... i totally had no idea what to write for the essays. Its supposed to be like... short answers apparently. But i wrote PAGES and PAGES of text. I'm not even sure if its relevant or anything... i just tried to make up for the lack of quality with quantity... which is so not going to work... the main problem is that i don't even know what the heck his qns where asking for. Mol evo was a really fun subject to study, but studying for the exams was tough work. VERY VERY LONG LECTURES. The lecture webpages were SUPER content FILLED. I took so much longer to go through each lecture than i did with any other course... Its like you just scroll endlessly through the text filled webpages... My friend printed out the lectures. One single lecture took like 16+ pages worth of text... Other mods had at most like... 10+ pages worth of SLIDES. NOT pages crammed with text. Bigg diff! Still, the essay qns were fun to answer. Hard, and i'm not sure if i understood him right, but i always liked these kinds of thinking qns.

Its like the biz law mod that i took too. My 1st ever open book exam, and also the last ever exam I'd be taking in a while - until i continue on with my pHd that is. I totally didn’t study for it at all... like... i couldn’t be bothered anymore cos it’s the last paper... plus i S/U the subject... plus it was open book... I made an absolute mess of my table and the shelf below with my textbook and all the notes... like my qn paper was buried under stacks of notes... and my notes were strewn all over the place i actually wasted a few minutes looking for them... but overall it was fun. always preferred thinking qns more than anything else... and since this was an open book exam, memorising stuff was not required... you just had to think on the spot, something which i really enjoyed.


FYP... hmm... did i talk abt it at all earlier? i forgot. But i must say i was really lucky... cos in the end i found two professors who were more than willing to have me. It was really a last minute kind of thing... one i met him the day before selection ends, while the other i meet on the day selection ends... still i was glad i made it in time. Kind of sad that in the end i didn’t pick the lab/chemistry based one... but its not that i totally dislike computer work... i had a genetics module in sec 4 options and we did n-blast and stuff and it was fun. For the project i'll be working on, i'll mostly be working on p-blast. I think the professors' really fun and hope i can learn a lot from them... gonna be working with belinda for my fyp.. we'll be working on diff genes, but the steps are basically the same so we'll be able to ask each other qns and stuff... which should be good for me... having someone to compete with is really something i've been lacking a lot since jc (jc i kinda gave up competing with anyone...)... and in uni i don't even know where i stand with my results... i know i suck, but i don't know how badly i suck kind of thing... another thing is that, we'll be working on 2 proteins each... if things goes well, the prof's hope is to publish one paper per gene... o.o don't know if things would really work out that way... only after that did i hear my other friends say stuff like how many profs seems to keep making loads of claims abt publishing papers etc as if using those as carrots to attract students... but it certainly didn’t sound that way when my sup said it. watever. that's not impt... what is impt is that i'll have to work my darn hardest... since it’s a computer based work, i can do it anywhere, any time... i can work as fast (or as slow ><) as i want... also, there's the promise that  if we finish the blasting work, we can go on to do labwork... so yeah, that's definitely a motivation for me to work harder. Really must thank belinda for introducing me to this prof. She was meeting another prof, but apparently that project had a lot of students visiting already, so the prof asked her to check out another project by my sup. Turns out that there was some kind of mistake and the project was not listed, no wonder they didn’t get any responses... They were looking for another student, so belinda asked me if i wanted to go meet the prof... which i did. I was genuinely interested in the chemistry project at nus too... it really feels bad having to decline the prof... he was really kind and explained the project in detail to me and all....

gonna meet my sup tmr at 5pm... can't wait for my fyp to start. 9th jan it shall be...