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BioGeeks tech meet, Science HackDay special

This month’s BioGeeks meeting at KCL is on Friday, June 18th, to coincide with the Science HackDay taking place over the weekend.

We have a special guest this month, Cameron Neylon, with an open-science-themed talk entitled “What have the public done for us?” Plus lightning talks on various subjects.

In other news, I’ve moved the blog over to the much cleaner and airier Barthelme theme. Drop a comment if it gives you any problems.


London BioGeeks — May Tech Meet is next week

The May tech meet is on Thursday 20th at Imperial College.

This month’s speakers:

Catherine CanevetOndex: Data integration and visualisation

Christopher BarnesABC-SysBio: Approximate Bayesian Computation in Python with GPU support

N. Purswani, L. Tweedy, Z. Patel, C. Suriel-Melchor — DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries

Does anyone have a link for DASbrick?

Drinks afterwards at Imperial’s Eastside Bar. See the BioGeeks blog for full details.


Back up all MySQL databases to separate files

Note to self — so I don’t have to think about it again next time.

export MYSQL_PWD=myrootpassword
DATE=`date -I`
for dbname in `mysql -uroot --batch --skip-column-names -e "show databases;" | grep -v information_schema`; do
	/usr/local/bin/mysqldump -u root $dbname | gzip -9 > $BACKUP_DIR/$dbname-$DATE.sql.gz
# Clear backups older than 7 days
/usr/local/bin/find $BACKUP_DIR/*.sql.gz -mtime +7 -delete

Edited to include compression. Remember to include full paths if you’re running it from a crontab, just in case.

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Google Chrome (actually Chromium) on Centos

Joy at last!

Chris Staite from the University of Birmingham has built a statically-linked version of Chromium, the open source version of Google’s Chrome browser, for Centos.

You can get it from here.

I was getting so sick of Firefox’s slowness and bloat, and Chromium is so much snappier, and more memory-efficient too.

Although to be fair, I don’t have nearly so many extensions installed yet…

It should just work out of the box with no extra dependencies to install. I’m using 64-bit Centos 5.4, and although it’s a 32-bit app, it seems entirely happy so far.

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Take Back Parliament demonstration — Sat 8 May

As someone who works with numbers, I’ve known for ages the electoral system in the UK is a very poor model.

The distribution of votes across the parties correlates very badly with the distribution of seats they get in return.

It’s possible, and not uncommon, for a party’s overall vote share to go down and yet its parliamentary influence to go up, or vice versa.

After years of adversarial flip-flopping, the system’s thrown up a result which nobody seems to be satisfied with, regardless of their party affiliation. (Except maybe the Greens :-) )

There are electoral reform demonstrations happening tomorrow, in London and all across the country:

If you can spare a few hours to go along, hopefully we can get a good turnout and make the case for real change while it’s still very topical — not the waffly kind of change that politicians promise every time and never deliver.

I’ll be in Trafalgar Square from 2pm.



London BioGeeks — April Tech Meet

This month’s tech meet is at 6pm on 21st April at University College London.

We have talks from…

Alison Cuff, UCL

The CATH database — Structural Diversity and the Question of the Fold Continuum

Andrew Martin, UCL

SAPTF — Sequence Analysis Plugin Tool Framework

John Pinney, Imperial College

GLASS — Gene LAyout by Semantic Similarity

Followed by drinks at 7:30-ish at the College Arms.

Full details, maps, directions etc. are on the BioGeeks blog.


Things to try when VirtualBox networking messes up

This is really a note-to-self but it might help other people too.

I have two network interfaces in my Ubuntu guest (on OS X 10.4 host), one NAT, one host-only.

Sometimes one of them doesn’t get an IP address — in ifconfig it has an inet6 address but not an inet address.

Today I tried

sudo dhclient eth1

and it worked — all it needed to do was re-query VirtualBox’s built-in DHCP server.

I would have thought this would do that automatically:

sudo /etc/init.d/networking restart

However that didn’t help… But dhclient did.

Another recurring problem is that when I move between different networks, DNS resolution gets screwed up. There’s a description of this with a suggested work around (using VBox’s DNS Proxy) here:

However, while this seemed to help with two of the networks I use frequently, it didn’t with a third, even after rebooting.

So, as suggested on one or two threads, I’ve removed the DNSProxy setting, and set the Ubuntu guest to use Google’s public DNS servers instead of those provided by the DHCP server for the NATted virtual NIC. (Blah blah blah.) Follow example here (more or less):

Seems to be working so far… But only tested on one of the offending networks, and without rebooting yet. Updates to come later.

… Nope, after upgrading to Snow Leopard and the latest VirtualBox (it’s now from Oracle — scary), random problems persist.

Sometimes I’ll lose guest-host connectivity in the middle of a session, without any sleep or other interruptions, but will still be able to see the internet from the NAT adaptor.

One possible solution here involving using OS X itself as the NAT router:

… but it’ll take work.

Or maybe a simpler version of the same approach: have a single host-only adaptor, use OS X’s internet sharing to share the AirPort card, and manually tell the vbox to use as the default gateway:

If all else fails, try using a different ethernet hardware emulator.

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NoSuchMethodError when running JUnit tests in Eclipse

This is worth a quick post as I couldn’t find a solution on Google and it took me an hour or two of fiddling.

I have a Maven project, call it frontend-war, which contains the main service code for FuncNet. A unit test kept failing in Eclipse with NoSuchMethodError, one of my least favourite screw-ups to disentangle.

In this case it was particularly frustrating, as the method (on a class in one of the main project’s dependent jars, called service-utils) definitely existed, was public, and had the right signature. Also, even more weirdly, when I ran the tests in Maven from the command line, they passed.

Cue all the usual Eclipse cargo-cult dead-chicken-waving — cleaning everything, closing and reopening projects, etc. etc. No joy.

Then it hit me… (solution below the jump)

Continue reading ›

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Solr presentation slides available

Tomorrow I’m giving a London BioGeeks talk about Solr, the Lucene-based search engine we’re using at CATH, and soon Smesh too.

The slides are available here (PDF, 500KB).

If you’re in London, come along, everyone’s welcome. Details here. We also have Manuel Corpas on KaryoDAS, and Phil Dawes on Git. And beer afterwards.

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Echoes of the past

In reflective mood, because it’s the end of the year, and prompted by some biographical reminiscences on Charlie Stross’s blog, I just found the contact details for my FidoNet BBS in an old nodelist from 1995.

Happy new year, everyone.