Long time no post!

It has been almost two weeks since I last made a post. I guess it's probably a combination of being busy with a mixture of activities and events. Last weekend was my Dad's birthday so I went back home to celebrate, after chilling out for a while we did a blind wine tasting session, which I failed abysmally at by picking the cheaper of the two wines under the belief that it was the more expensive one. My only excuse was that I didn't have a pallet cleanser. Anyway we went out to a Turkish restaurant (for a change, we normally go to Chinese for some reason) in the centre of Notts. We all went for the 3-course meal, greater starter - mixture of beans, sauce, salad. I had a traditional mixed kebab for the main course then finished up with some bakala (if that's how you spell it?). All in all a good night. Sunday I decided to go down to SOS with my brother. I thoroughly enjoyed it, the level 4 lesson was good- good in the sense that it pushed you but was not out of your league.

Other news

More recently I have been offered a post-doc position, so that's great news. The thesis seems to be going well, just a bit of chopping and changing then all should be done and dusted.

In the mean time I need to sort out a presentation for my PhD for tomorrow and get a pizza from the shop, so I can't procrastinate any longer!

An Interesting New Paper

Titled: “Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem.”

Authors: M. Karthikeyan, S. Krishnan, Anil, Kumar Pandey, Andreas Bender, and Alexander Tropsha.

Provisionally published in JCIM.

A long story short, they have published the first online open source distributed computing and data analysis architecture written in Java using the remote method invocation. The resource can be found at:

http://moltable.ncl.res.in/chemstar/index.jsp

The network consists of 25 windows based machines. Server side computing requires Java, Oracle, MySQL or MS Access. On the client side only Java is required.

They have demonstrated its ability by calculating descriptors on a dataset of over 11 million compounds using the JOELib and Marvin toolkits. At present they are able to calculate: pKa, log P, log D, polar surface area, charge distribution, polarizability, topology analysis, H-bond acceptor, H-bond donor properties, the prediction of protonation microspecies, Huckel analysis, refractivity and elemental analysis. They envisage extending these methods to in-silico-based virtual screening, fast docking, text mining or other related informatics applications.

I am also very interested in this work as their homepage (see link above) is written in Java Server Pages (JSP), a language I have started to write some open source web services in.

Web Site Crashing!

What a day! I woke up a little late then went into town to get a collection of clothes for the spring/summer. After looking around numerous shops I decided on two tops from Next. One a v-neck with a shirt, the other a t-shirt/hooded top cut off at the sleeves.

The rest of the day as been spent browsing the internet and listening to music. I must admit since I have spent a reasonable amount of time browsing the web today I am not particularly happy with the fact that the web server I am hosting my website on has effectively crashed for the most part of the day. I suspect that now that I'm not using so much bandwidth they will move me to a slower less robust server!

So if anyone was trying to access my page today, I would like to apologise for the inconvenience!

Online classification tools

I have just set up some online classification tools based on the WEKA machine learning library.
More information can be found at: http://edcannon.hobby-site.com/SimpleUpload.jsp .

Basically people can upload one file upto 5mb in size and then use either: SVM, NBayes, Logistic, k-NN (k=1), RandomForest or the PART rule based learner.

The results are based on the default parameters in WEKA and using 5-fold cross-validation.

I hope some people might make use of this facility!

Birthdays Galore

It appears that everyone has a birthday in April. Dub last Saturday, Nicola today and Florian tomorrow. I think Florian wants to go for a meal somewhere then off to La Raza for a few cocktails, not sure, but I'm sure he's got it all ironed out.

Yesterday I decided to treat myself to a haircut - it was about time. The barber that I regularly go to is apparently moving shop back into the centre of Cambridge, so that means I might need to go into the centre, which is a bit of a pain or alternatively find a barber closer by.

On a different note:

Chemoinformatics
Currently looking at new webservices, more information on XML and CML processing and XOM.

Salsa
I had a good time last night at the Slug and Lettuce, the dancing and the lesson were enjoyable.

Webservices

Initially I thought today was not going to be such a productive day. However, I have now managed to set up an online web server http://edcannon.hobby-site.com/CDKDescriptorCalculation.html) that can calculate descriptors from the Chemistry Development Kit given a smile string as input. The descriptors that have been implemented at present are:

• BCUT
• Fingerprint
• Apol
• Number of aromatic atoms
• Autocorrelation descriptor with polarisability
• Number of hydrogen bond acceptors
• Number of hydrogen bond donors
• Lipinski's rule of 5
• Total polar surface area
• XlogP

More descriptors will be made available later. I also intend to put an online service for machine learning algorithms in using the Open Source WEKA Java library.

Off to bed.

Dub's Birthday

After a day in the lab reading papers, I was off to the Mitre pub to celebrate Dee's birthday. Florian and I initially went to the Prince Reagent then on to the Avery to get food, but had no success. It's surprising how early pubs stop serving food, particularly at weekends in Cambridge. Anyway we managed to go to the GBK, I had a thai burger (red thai sauce), tasted great, but quite expensive. In the region of £10 for a diet coke and a burger.

We then ended up at the Mitre ~9pm had a drink there, then Florian's friend Michael came, he seemed to be happy and in high spirits [like Flo, me and Dub....not so sure about everyone else though]. Two drinks later we tried La Raza, but at £6 to get in, the ~£7 per cocktail we parsed on this and ended up in the Fountain where Steph joined us later. I must have stayed till about 1am before I got too tired of dancing and talking.

Today I was meaning to go to the gym. However Queens' College have still not sorted out where the gym key as gone missing or who has it. If this turns into a more regular event I may decide to join a different gym. In the end I went for a run around Granchester as the weather was great tonight. I think we're going to be in for some sleet and snow on Mon, Tues and Wednesday. Snow in spring...shocking.

Bowmore More More!

Our whiskey guide last night was Andrew Torrence, he took us to the Isle of Islay for two different types of single malt. On this tour was myself, Zhenzhi, her friend, Volker and about 10 others.  All in all we had 6 different whiskeys. The line up:

Auchentoshan - 10 year old

Auchentoshan - Three Wood

Bowmore - 12 year old

Bowmore - 15 year old

Bowmore - 18 year old

and the mystery guest: Bowmore 25 year old.

My favourite was the 18 year old, quite sweet -evident from the sherry cask, with a strong peaty after taste.

Zhenzhi liked the 25 year old, the only noticeable improvement in this whiskey was the length of the after taste and at £250 pounds a bottle I was not prepared to buy that! Maybe when I'm richer.

==The Good Tasting Guide - 6 Steps==

1. Look at the colour of the whiskey- indication of the cask its been in.

2. Swirl the whiskey in the glass, see how wide and long the legs are (the wider and longer, the older the whiskey).

3. Take a small sip on your tongue, let it evaporate, the length of time it takes to evaporate is a measure of the alcohol content.

4. Smell the whiskey.

5. Drink the whiskey - initial reaction on tasting / swallowing.

6. The after taste in your mouth.

Zhenzhi and I then ended up a Club Salsa for some dancing, which given the fact we had that much whiskey, I think we did quite well.