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Update – 21/01/2012: added non-breaking space, and minimised regex.

/([.!?]|<p[^>]*>)(\s|&nbsp;|<br\s*\/?>)*/

I am using the above regex in a PHP function to find the beginning of a new sentence or paragraph in HTML, as part of a WordPress plugin I’m currently developing. The regex looks for sentence-ending punctuation (.!?) or a paragraph tag, followed immediately by 0 or more white spaces or HTML line break tags.

I’m particularly interesting in finding the first letter of the new sentence or paragraph, hence allowing for the possibility of white spaces/ line breaks.

I don’t claim that it’s perfect… but it’s working so far. I will improve the regex as and when necessary.

Thanks to Hidayath for help in formulating the regex.

The prospect of using the genome as a universal diagnostic is upon us TODAY.” – Richard Resnick

A recent technological revolution means that any regular ‘Joe Bloggs’ could have their genome completely sequenced for a few hundred dollars in the very near future. What implications will that have on health care, politics and even relationships?

I just heard about this job expo for scientists taking place in London next week!

Now in its fifth year, the Naturejobs Career Expo is the UK’s largest career fair and conference for the scientific world.

The Expo promotes the UK and Europe as great places to pursue a career in science, be it in industrial research, research organisations or academia. It presents the best opportunities from the best organisations: public, private, national and international.

Jobseekers can meet with potential employers offering hundreds of genuine vacancies. The conference plenary and workshop sessions will provide a unique opportunity to meet high profile scientists and gain careers information and advice.

Over 1000 experienced UK and European scientists, in physics, chemistry, the life sciences and medical sciences, actively seeking their next career move attend.

I’ve been using NatureJobs as a main source of bio-related job listings for a few years now. It looks like a worthwhile trip for students, graduates and research veterans alike.

The exhibition and workshops are free, but you need to register. You have to purchase a ticket if you want to attend the conference – unfortunately, you might find £50 a bit of a hefty price tag if you’re out of work.

I haven’t used Adobe Flash Builder 4 since March. Between then and now, my MacBook has been upgraded to OS X 10.6 by the Apple Store after yet another hard drive failure (!). I launched FB4 last night, and faced a whole bunch of error messages which I didn’t save, unfortunately, but I did see the word ‘java’ popping up here and there.

This reminded me of the fix for a release build issue I faced a while back, which involved deleting the xerces.jar located in user.home/Library/Java/Extensions/. After reinstalling FB4, I deleted said file, and the launch errors have disappeared.

I don’t know what said JAR file contains, but it does seem to be causing FB4 a lot of problems!

Update: while searching for the fix, I came across this article on how to speed up Eclipse on Snow Leopard.

I was emailed info on the following grant from a representative of the Integrated Biology team at Agilent Technologies, Inc. Though the amount is advertised in USD$, the grant application is open to academic institutions outside of the US.

Fostering integrated, whole-systems approaches to biological research with two $75,000US grants for open source data-integration tool development

The different omics platforms—genomics, transcriptomics, proteomics and metabolomics—are generating new insights into how biological systems work at a molecular level. Although each individual omics approach provides a global view of a specific cellular process, this view is limited to only one aspect of the biological system. In order to gain a comprehensive understanding of the system as a whole, researchers are faced with the challenge of merging these very different data sets.

Agilent is supporting scientists who are taking on this challenge through our eMerging Insights Grant Program. We currently have two open initiatives for academic and non-profit researchers developing and/or improving open source, Agilent-compatible software tools to integrate multi-omics data. Each initiative will provide $75,000US to a single academic or non-profit research lab in fiscal year 2011. A proof-of-concept prototype or working solution must be demonstrated at the end of one year, using either existing data sets from the investigator’s own lab or institution, or from new or existing datasets produced at Agilent.

One of the most important outcomes of our eMerging Insights Grant Program is the development of open source* solutions for the analytical life science community. Any tools developed with this funding will be freely available, open source tools for the research community.

The submission deadline for these two initiatives is August 12, 2011.

Awards will be announced September 30, 2011.

*All free or open source licenses are acceptable except “any license requiring , as a condition of use, modification and/or distribution of the software subject to the license, that the software or other software combined and/or distributed with it be (i) disclosed or distributed in source code form; (ii) licensed for the purpose of making derivative works; or (iii) redistributable at no charge. Excluded licenses include, but are not limited to, the GPLv3 License.”


Visit the Agilent site to download the application form.

Link to forum post:

I’ve been unable to export release builds of any AIR projects when using a Mac installation of Flash Builder 4. I can run the AIR apps within the IDE, but I keep getting the following error when exporting: “One or more errors were found while trying to build the release version. Unable to export.”
The weird thing is that I can export the exact same AIR projects using my Windows 7 copy of FB4 just fine, without any errors.

Details of the Mac installation:
OSX 10.5.8
Flash Builder 4 plug-in version, v4.0.1, on Eclipse v3.4.2

I performed a fresh install of FB4 today (before anyone suggests it :) but to no avail.

The error log – I wasn’t sure what to copy, so just took everything that had the right time entry:
Continue Reading on the Adobe Forum…

Update (01/02/2011): I discovered the fix!

I Googled the error message: “org.apache.xerces.dom.DeferredElementImpl.getTextContent()Ljava/lang / String”, and came across the following bug report:
http://code.google.com/p/alkwarel/issues/detail?id=10

As suggested in the link above, I deleted the xerces.jar located in user.home/Library/Java/Extensions/. I then cleaned my project, and FB4 for Mac finally exported the release build!

I am pleased, yet also sad to see how many hits that one of my earliest posts, “Connecting Flash Builder 4 to MySQL using Java” regularly receives via search engine referrals. Happy, because I’m always happy to help! Sad, because clearly a lot of people still need help connecting their Flash Builder app to a database.

MySQL is a reliable platform if you wish to store large amounts of data, for access by multiple users. However, if your schema is simple, and you don’t require lots of bells and whistles, you may want to consider simplifying your life, and using SQLite with an AIR app instead.

From the SQLite About page:

SQLite is a in-process library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine. The code for SQLite is in the public domain and is thus free for use for any purpose, commercial or private. SQLite is currently found in more applications than we can count, including several high-profile projects.

SQLite is an embedded SQL database engine. Unlike most other SQL databases, SQLite does not have a separate server process. SQLite reads and writes directly to ordinary disk files. A complete SQL database with multiple tables, indices, triggers, and views, is contained in a single disk file. The database file format is cross-platform – you can freely copy a database between 32-bit and 64-bit systems or between big-endian and little-endian architectures. These features make SQLite a popular choice as an Application File Format. Think of SQLite not as a replacement for Oracle but as a replacement for fopen().

The best part for Flex developers is that AIR has native integration of SQLite. Creating a local database for your AIR app couldn’t be easier, as you write out your SQL commands within ActionScript itself: click here for a sample script. No Java, no Tomcat server, and no BlazeDS required! Yey!

As part of its vision to promote world-class interdisciplinary research to tackle Grand Challenges such as Global Health, UCL has created a number of research centres and institutes, which have been brought together to form the UCL Computational Biology community.

To formally launch this community, a Symposium will be held on Tuesday 15th February 2011 from 9.15am to approximately 5.30pm, in the Christopher Ingold Auditorium, Department of Chemistry, University College London. A poster session and post-Symposium Reception from 6.00pm, will be held in North Cloisters, Wilkins building.

Please note the closing date for registration is Tuesday February 1st. Registration on the day will take place outside the Christopher Ingold Auditorium, Department of Chemistry, from 8.45am.

The program of speakers include: Steve Oliver (keynote), Angus Silver, Sally Price, Mark Girolami, Mark Thomas, David Balding.

Click here to book your FREE ticket. Registration open till Feb 1st, 2011.

Here’s a tip for making a SELECT statement that little bit more flexible. Thanks to Kevin Bryson and Hidayath Ansari for sharing it with me.

The Problem: I want to select all the rows from example_table, where at least two out of three of the following conditions are true: column_a =1, column_b = 1, and column_c =1.
View full article »

Free Online C# Tutorial

I started a new job a couple of months back, and with it came new challenges, including the task of learning yet another language, C#, which looks a lot like Java, but the end program can only be used on the Microsoft platform.

I have a copy of Visual Studio 10 installed on a shiny new Windows 7 laptop (thanks to my generous employers), and I’m using this free online tutorial to familiarize myself with the basics, as preparation for an advanced, two day training course… that starts tomorrow!

I hope to post some C# tips, tricks and code over the next few months, as I did before with Adobe Flashbuilder.

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