I’ve just uploaded my Perl scripts from Summer ‘07, when I was doing my MSc. dissertation on a possible new method for predicting the pharmacologically important property logP in a large database of potential drug candidate molecules.  These descriptions aren’t great, a more in-depth explanation of how they were used will be forthcoming, just in case there are any budding computational chemists out there who would like some Perl examples specifically geared to their field.  The CSV parsing routines are probably the most useful, as they can be easily adapted to different data structures and don’t require any external programs.

CSVparser – Contains all the CSV parsing functionality that I needed.
colappend – Appends a new column from a specified input file to an existing CSV file.
XEDcompoundfilter – Removes lines from an XED output file where there is no data, and also according to an optional blocklist of SMILES strings (used to remove outliers).
XEDparser – Parses an XED output file in a variety of ways to generate the required CSV file.
XEDrunner – Handles the conversion of SMILES string files to XEDEX input files, runs them through the XEDEX program and then the SDF conversion program to produce readable SDF files.

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Right, I haven’t blogged for ages so here’s the f’shizzle:

I recently moved from Edinburgh back down to Sheffield, staying at Richey’s while I started my job and found somewhere for me and the girly thing to live… I’m working for School Trends doing 2nd Line Web Technical Support, basically fixing stuff that the customers (mainly schools) have problems with, in managing their websites. What’s cool about it is I can try my hand at pretty much anything that helps to make the software or customer experience better, which is quite liberating, although the requirements of the position will relegate my coding explorations to only a few hours a week. I’m still ultimately aiming to be able to do Web App development, so any R&D or general developmental experience at School Trends will be great and I’ll jump on any chance to make their software better and help with redesigning the UI.

The new abode will be in Ranmoor, which is particularly poncey – as is the flat It’s about 45-55min walk out of town, from what I can tell – which isn’t quite as close as I originally wanted but it’s an awesome area and the flat is seriously phat. It’s really hard to get decent flats in nice areas much closer to town. Hopefully I should have all my junk moved up from dearest mama’s by early January too.

This site hasn’t had much done on it at all recently besides finally fix the menu to a point where I’m actually rather pleased with it; I am however getting a lot more confident with PHP & MySQL so it should take less time to roll out things that I want put on the site. The quote generator test I did worked fine, which means that the random image generator will take only about 5min to do, given that the code is quite basic and pretty much the same thing. The main thing I will be working on before both of those are live is the login system, I need it to be as close to the LoginView .NET control as I can get it in terms of functionality. SEO is also a priority; I really need to get my Google listing sorted. Hopefully by the time I’ve got somewhere with those I’ll have some more content (I know, it’s crazy talk…actual content on my site!), and then I’ll probably do that AJAXy Photo viewer along with some Semantic Web stuff.

Edit:

Little did I know that being entirely responsible for the development of a CMS, as well as most technical support issues for over 200 customers, would completely demolish my appetite for spending time developing this site.  A few months ago, one of the Mozilla developers blogged about losing his interest in developing Firefox extensions due to spending most of his working day hacking on the ‘fox.  I totally empathise with this, although I don’t plan on giving up on this site just yet.  So:

• Photos will happen eventually, although I’ll probably grab someone else’s viewer code and customise it a little.
• Login system has been dropped as it was rather ambitious and probably would not have been used much anyway.
• Changes to the design are now mainly restricted to CSS bug fixing.  If/when I get bored of the design, I will either make gradual changes or, if I want a fairly substantial change, will just pick a nice WP template.
• I can’t be bothered to make this site work in IE6, I spend enough time doing that at work.  Anything to hasten it’s demise…
• The GridView tutorial won’t be happening – I’m not in possession of it, I’ve tried numerous times to get my hands on it in some form but to no avail.  It is a pity as I spent ages on it and it would have been a great addition to the site, along with a good way to reacquaint myself with .NET, but ’s been quite a while so I’ll just let it go now.  I have some other things in the pipeline to help flesh out the Downloads page.

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Listening to: Kayo Dot – The Antique

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Ok…so I’ve been rather silent here. I’m still alive, currently living in Edinburgh with my new lady (who is the best thing to happen to me in a very long time). The MSc and DoD (Dissertation of D0000000m) have ended and I am sans job. I’m involved in a concerted effort to get a position in web development as I’d like to work in an area that

• I’ve always been fascinated by
• I actually enjoy
• Isn’t science (I’m fed up with research after the DoD and want to see what else there is)

The site has come along a great deal since I last wrote something here, with eleventy billion bug fixes and extra features, and some actual design work has happened to ensure that it doesn’t look like a pile of junk. It’s far from finished – I have several little bits yet to do, along with the mildly irritating task of getting it to look nice in the abomination that is IE6. In fact I would have done the IE6 testing already if M$ hadn’t made it impossible to run it in Vista; as it is, I have to install 1.5+Gb of virtual OS (XP SP2) to get anywhere near IE6. So I’ve decided not to bother and to gopher the prettiest Linux ever (Kubuntu) and WINE instead. After these job applications. Job > IE6 compatibility.

Anyway, here are the main recent improvements to the site:

• Cool PHP breadcrumbs script added to generate crumbs from directory structure
• Even cooler browser-specific, dynamic PHP generated CSS and JS files – this was a lot easier than I thought it would be to implement. I’m sure this puts a hefty load on the server, but I can’t see it causing any problems, unless I start getting lots more hits.
• Tutorial for my scrollable, sortable table – hopefully *fingers crossed* I can get my GridView tutorial up here too. I also have some Perl scripts to put up, just data juggling stuff but some budding computational chemist out there might find them of use
• Clicky-sprouty hidden JS divs for code and suchlike – sadly not yet working in Opera, but that’s not so bad (sorry, Opera users)
• Vastly improved menu
• Much better Smarty code, making it far easier to change (and add) pages to the site
• Smarty templates seamlessly hooked into blog files through some carefully placed PHP includes – again a lot easier to do than I anticipated
• Nicely formatted CV page that kicks the bottom of my existing CV – I will back-port the changes to the document version shortly and put it up here for download
• Contact page that works and works well, I’m sure the JS validation script can be improved but it’ll do for the moment.

The Wordpress update to 2.3 didn’t work (both 1-click & manual) so I’ll stick with 2.2.1 until I figure a workaround (probably best backing up, deleting and re-installing). More to come.

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Is a bit of a mad month so far.  My MSc dissertation at Eli Lilly is starting to come together, which means it’s starting to get hectic as I’m trying to make sure I write things up as the results appear.  I’ve started applying for jobs too, anywhere and everywhere so who knows where I will end up.  I’m just getting to know this area so it would be nice to stay here, or go back to Sheffield which I really enjoyed.

Just done some more work on the site, the development version now has a fully functioning AJAX throbber which I will be utilising in my AJAX picture viewer.  I hope to get the first (quite limited) version of the site up and running this week.

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