The elevator pitch goes something like this:

“The project extends existing blogging tools for use as a lightweight, semantically linked publication environment. This enables researchers to create a hub in the linked-data environment, that we call knowledge or k-blogs. K-blogs are convenient and straight-forward for authors to use, integrating into researchers existing work practices and tools. The provide readers with distributed feedback and commenting mechanisms. We will support three communities (microarray, public health and workflow), providing immediate benefit, in addition to the long term benefit of the platform as a whole. Additionally, this will enable a user-centric development approach, while showcasing the platform as the basis for next generation research publishing.”

If this sounds like the kind of thing you’re interested in, Phil has made the full grant application that we submitted available online, on knowledgeblog.org. We would of course be interested in any comments or feedback. The proposal includes some technical details of what we hope to achieve, but I think that Ontogenesis has already gone some way to proving the worth of the system. It’s going to be great to provide additional tooling to support the process, and cement some of the inherent social contract with a proper workflow for publishing and review.

The  project starts almost immediately, and knowledgeblog.org will be the place to stay tuned for updates.

GeneSpring GX 11 is the third iteration after Agilent bought up Silicon Genetics, then decided to throw the unwieldy, quirky, but very functional GeneSpring product in the trash and start again with something built on Strand Life Sciences AVADIS platform.  We’ve been through versions 9, 10 and now we’re on 11.  There’s been plenty of bugs on the way, the most serious (to me) being the one where GeneSpring 10 managed to miscall the quality flags on Illumina data in 50% of the cases.  Not good, but at least fixed.

Many people have been griping on mailing lists about functionality missing in the new GeneSpring that existed in the old version.  I always think it’s a matter of familiarity with the software really.  I hadn’t really come across anything I couldn’t do in GeneSpring 11 that I could do in GeneSpring 7.  That was until yesterday.

I sat down with a customer yesterday to look at some microbial Nimblegen data.  GeneSpring doesn’t really deal with Nimblegen data very well, you are left with the choice of not analysing it in GeneSpring, or accepting there’s going to be a bit of fudging and some extra annotation steps in order to make the data useable as a ‘Custom technology’.  The customer, quite reasonably, asked if we could get the biological genome information (effectively gene annotations that are independent of the chip technology you’re using) loaded into GeneSpring.  And thus started a morning of fun and games.

GeneSpring 11 has a very handy import feature for biological genomes under Annotations>Create Biological Genome.  That is providing you want to choose one of their predefined organisms to download the information from NCBI.  There is *NO* route in the software to add another organism to this list, or do anything than use one of their check box limited organisms.  This is not a bug apparently, because in a separate part of the software (dealing with Pathways for an organism) you can pull this information directly from NCBI using the Taxon ID of the organism you’re interested in.  So why can’t you use it to download a biological genome?  Who knows…

One of the things I really liked about the old GeneSpring was the fact that it came with a manual a foot thick.   It told you how to do every single operation in the UI, it didn’t tell you anything about the order in which to apply them, but you could generally rely on it for an answer.  There was no such answer to this issue in the GeneSpring manual..

It transpires that if you really want to do this, the following, slightly insane process needs to take place:

1) Take this snippet of XMLishness:

<hexff version="1.0">
<object type="cube.plugin" version="1.0" handle="0">
 <key>type</key>
 <string>plugin.product.TaxID</string>
 <key>id</key>
 <string>TaxID</string>
 <key>data</key>
 <!-- taxID.xml for various organisms {{{ -->
 <dict>
 <key>Homo sapiens</key><string>9606</string>
 <key>Mus musculus</key><string>10090</string>
 <key>Rattus norvegicus</key><string>10116</string>
 <key>Anopheles gambiae</key><string>7165</string>
 <key>Arabidopsis thaliana</key><string>3702</string>
 <key>Bacillus subtilis</key><string>1423</string>
 <key>Bos taurus</key><string>9913</string>
 <key>Caenorhabditis elegans</key><string>6239</string>
 <key>Canis lupus familiaris</key><string>9615</string>
 <key>Citrus sinensis</key><string>2711</string>
 <key>Danio rerio</key><string>7955</string>
 <key>Drosophila melanogaster</key><string>7227</string>
 <key>Equus caballus</key><string>9796</string>
 <key>Escherichia coli</key><string>562</string>
 <key>Felis catus</key><string>9685</string>
 <key>Gallus gallus</key><string>9031</string>
 <key>Glycine max</key><string>3847</string>
 <key>Gossypium hirsutum</key><string>3635</string>
 <key>Hordeum vulgare</key><string>4513</string>
 <key>Macaca mulatta</key><string>9544</string>
 <key>Magnaporthe grisea</key><string>148305</string>
 <key>Medicago sativa</key><string>3879</string>
 <key>Medicago truncatula</key><string>3880</string>
 <key>Nicotiana tabacum</key><string>4097</string>
 <key>Oryctolagus cuniculus</key><string>9986</string>
 <key>Oryza sativa</key><string>4530</string>
 <key>Ovis aries</key><string>9940</string>
 <key>Pan troglodytes</key><string>9598</string>
 <key>Plasmodium falciparum</key><string>5833</string>
 <key>Pongo abelii</key><string>9601</string>
 <key>Poplar mosaic virus</key><string>12166</string>
 <key>Populus sp.</key><string>3697</string>
 <key>Pseudomonas aeruginosa</key><string>287</string>
 <key>Saccharomyces cerevisiae</key><string>4932</string>
 <key>Saccharum officinarum</key><string>4547</string>
 <key>Salmo salar</key><string>8030</string>
 <key>Schizosaccharomyces pombe</key><string>4896</string>
 <key>Staphylococcus aureus</key><string>1280</string>
 <key>Sus scrofa</key><string>9823</string>
 <key>Takifugu rubripes</key><string>31033</string>
 <key>Lycopersicon esculentum</key><string>4081</string>
 <key>Triticum aestivum</key><string>4565</string>
 <key>Vitis vinifera</key><string>29760</string>
 <key>Xenopus laevis</key><string>8355</string>
 <key>Xenopus tropicalis</key><string>8364</string>
 <key>Zea mays </key><string>4577</string>

 </dict>
 <!-- }}} -->
</object>
</hexff>

2) Add an entry

<key>Your organism name</key><string>NCBI Taxon ID</string>

after the Zea mays line

3) In your GeneSpring directory under this tree:

GeneSpring  GX11\bin\packages\marray\project\2.1

Create a folder called ‘plugins’ and save the edited XML above as a file called TaxID.plg

4) Restart GeneSpring and proceed to update your newly added Biological genome, which now appears in the list!

Actually, I have to say, I’m not sure I ever want to see that in a manual of a piece of software as expensive as GeneSpring…  And besides this still doesn’t work for me as advertised because GeneSpring, whilst aware of what an HTTP proxy might conceivably be, has no concept of what an FTP proxy might be – which is problematic when you need to connect to ftp.ncbi.nlm.nih.gov.  Brilliant!

I am however a supporter of the “Sense about Science” campaign.  Any organisation dedicated to fighting crackpots, frauds and pseudoscientists is going to find favour with me.

I do urge everyone to go and sign the ‘Keep Libel Laws out of Science’ petition here. Have a read, have a think. Is this the way we want things to continue?

BioSysBio had been recommended, and not least because we had a Newcastle student member on the organising committee.

BioSysBio is a relatively new conference run by the Institute of Engineering and Technology.  I admit I had been largely ignorant of the IET, probably because I’m not an engineer of any sort, and it’s a professional body for the engineering community.  BioSysBio, being a conference largely focused on systems and synthetic biology actually falls quite well under the engineering remit – not just for the engineering approaches that are applied to synthetic biology, but also because sometimes, just sometimes this kind of work needs giant, room-filling robots.

The meeting this year was held in Cambridge in the UK, one of our most venerable university towns, giving the event a feeling of academic history despite being about possibly the most cutting edge of biological sciences.  Over three days a group of probably 250 people gathered in the Music Department to discuss, listen, type, debate and network.  A word to other conference organisers, holding the conference in the Music Department is a great idea when you have a conference venue designed for performance – the acoustics were great for talks.  The lack of power supplies however belied the number of concert goers that normally need to plug in a laptop and work whilst they listen.  A reminder to us all that it’s all very well packing our power adaptors when we go to a conference, but a four-way block/gang plug would make you a popular person indeed in situations like this.

I don’t want to run over all of the sessions, you can find the programme for the three days here.  I do however just want to rave about how good a conference this is, and share a few highlights.

At the moment BioSysBio is a great size, and is run as a single track conference with unconference style breakouts given their own slot.  A two hour slot on the second afternoon was given over to a number of simultaneously run workshops (I plugged for the ONDEX tutorial, because I work with some people who are on the ONDEX project – but still had no idea how to use the software).

Interestingly there was a really good balance between the systems biology and the synthetic biology sides of the track.  I was more impressed by the lack of laptops being sported during the talks, it meant that actual, real biologists were present mixing it up with the informatics and mathematics geeks.  This also showed through in the poster sessions.  It’s a refreshing change for a bioinformatician to see the science that has resulted from informatics based approaches, rather than having the implementation of the approaches being the primary concern.

My talks highlights came from a number of people and areas.  I found Julian Huppert‘s talk on “Four-stranded DNA: How G-Quadruplexes control transcription and translation” fascinating.  Here was a whole area of transcriptional control I had never even come across, mediated by DNA structures I had never heard of.  That’s one of those nice eye-opening moments at a conference, when the complexity of the systems you study is just laid bare in front of you by something new and exciting.  On the second day we had a talk entitled “Effect of pauses on transcriptional noise” from Andre Riberio, following on from a previous talk on RNAP the previous day by Marko Djordjevic.  The idea of patterns in transcriptional noise, caused by kinetic and spatial restraints really caught my imagination.  I really enjoyed Catherine Lloyds talk on CellML – we’re interested in both SBML and CellML at Newcastle, and it’s always nice to see speakers from both projects on the same billing.  The panel discussion on security and synthetic biology (and touching on DIYbio as well) was extremely enlightening and not just because of the fantastic talk by Drew Endy who I had the pleasure of seeing speak twice at the meeting.  On the final day there was much to chose from from Christina Smolke talking about building circuits with bits of RNA to Piers Millet from the UN talking about why we should care about securing synthetic biology.

This brings me nicely onto online coverage of the conference.  If you want to read blog posts about any of the talks, there’s just one place to go and that is to Allyson Listers blog at lurena.vox.com.  Ally, who we shall now refer to as the ‘Robot Blogger’, managed to have coverage of each talk online within minutes of them finishing, whilst apparently being able to type up notes from the talk immediately following this.  When Allyson spoke about her work on SAINT, Simon Cockell of FuzzierLogic picked up the blogging slack.

The conference organisers were fully Web 2.0 enabled.  We had a pre-existing room on FriendFeed that got heavily trailed on the first day, as well as a small contingent of Twitter enabled users contributing comments and commentary during the talks.  These were all aggregated with the hashtag #biosybio.  I think everyone agreed that whilst this is never the best way to present information from a conference (doing this on Friendfeed with an agreement between participants in a threaded discussion probably the best) I know that those of us who were twittering away were at least being thanked for it from others who could not attend.  That certainly kept me interested in how my wifi connection was doing throughout the day.  We also had the strange effect of some of our colleagues and former colleagues attending “The Influence and Impact of Web 2.0 on e-Research Infrastructure, Applications and Users” at NESC who were all using the hashtag #research3 and we even had some microblogging cross talk going with delegates there.  That was a new one for me certainly.

Despite not everyone on my Twitter subscription lists being a scientist, let alone ones interested in synthetic or systems biology, and despite posting hundreds of very geeky tweets, not a single person unsubscribed from my posting frenzy.  Either no-one is paying attention or people were happy to filter the noise for a couple of days, which I thought was great.

To sum up, it’s a great conference.  It will be great to go to it again next year in Oxford too.  I can’t remember the last time I attended every conference talk, even the 8.30am ones.  I can’t remember the last time I went to a conference and wasn’t tempted to have a post lunch snooze in the lecture theatre afterwards.  I can’t remember coming away from a conference so fired up and so keen to get back to work and start thinking harder about this years iGEM competition.  Actually the last conference I felt anything like this much fervour and excitement about was the excellent (but never repeated) O’Reilly Bioinformatics Technology Conference in Tucson in 2002.

Next year, if you’re in the field, or even vaguely interested in the field, beat a path to this conference in Oxford.  Beg, borrow or steal the cash.   I will see you there.

This morning, poking around on the ‘Listen Again’ part of the site, I found the embedded Flash players that would allow me to listen to the podcasts in my browser.

I wanted them to listen to on the way to work however!

A bit of digging around through the HTML and subsequent XML playlists, I managed to find downloadable, transferable mp3 content.  Linked here for your listening pleasure:

Programme 1

Melvyn tells the story of Darwin’s early life in Shropshire and discusses the significance of the three years he spent at Cambridge, where his interests shifted from religion to natural science.

Programme 2

Darwin’s expedition aboard the Beagle in December 1831 and how his work during the voyage influenced and provided evidence for his theories.

Programme 3

How Darwin was eventually persuaded to publish On the Origin of Species in November 1859 and the book’s impact on fellow scientists and the general public.

Programme 4

Melvyn visits Darwin’s home at Down House in Kent. Despite ill health and the demands of his family, Darwin continued researching and publishing until his death in April 1882.

Happy timeshifting Darwin Day!

A good hub for information on the celebrations would be the Natural History Museum’s Darwin200 site.

I was glad leafing through Chris Miller’s blog today to find out that I’m not the only scientist who has actually never read this book.   I actually downloaded the text from Project Gutenberg some years ago and stuck it on my iPod (in the days before I carried a smartphone) with the intention of reading it.   It was too long for the iPod reader, so I never got around to it.

In the absence of any formalised New Years Resolutions I promise to go out and find a nice hardbound copy to grace my bookshelf.  And read it too.

However, it’s not the only scientific anniversary being celebrated.  For those people who are more interested in staring at the sky than staring at living organisms 2009 is also the International Year of Astronomy.

Again, there’s a fantastic dropping off point from the IAU and UNESCO at astronomy2009.  But why is this being celebrated?  In this case it is the 400th anniversary of the first use of an astronomical telescope by Galileo Galilei, whose legacy is at least as awe inspiring as that of Darwin’s.

With an amateur telescope setup with a CCD camera/webcam capable of producing pictures rivalling that of a 200″ telescope in the 1950′s I always feel it’s a shame that more people don’t stare in awe at the sky.  I particularly liked this story on the Physics World site, about how a group of people are going to build a replica of Gallileo’s telescope and image through it, to show what the man himself might have been capable of resolving.

I find it interesting that these are both thinkers who proposed theories that were against the prevailing religious orthodoxy, and in Darwin’s case some even now failing  to be accepted by some people of a more closed minded religious persuasion.   Maybe all Darwin needs is another 250 years?

Whilst I’m making ad hoc resolutions – I will also use this year to  interact more with my local astronomical society, a group of people who I am in frequent email contact with, but have yet to pitch up to the society meetings to join.

I’m proud to be a scientist, and I’m proud of the wonderful achievements science has made, so it will be nice to use these two excellent celebrations to push my own knowledge forward a little more.  And not just focused around the computerised science I spend my time on.

Ever heard of “Murine” products as in “Murine Dry and Tired Eyes“?

Maybe I’ve been living in the dark, since I don’t wear contact lenses – but this does strike me as being a particularly bad name for a product.  Fine, so I spent years at the bench, a genuine ‘lab rat’ but I can’t imagine that I am the only person who thinks that murine means:

of or relating to a murid genus (Mus) or its subfamily (Murinae) which includes the common household rats and mice; also : of, relating to, or involving these rodents and especially the house mouse

I would love to know what rationale there was for not looking up the word ‘murine’ in a dictionary before naming your product.  Is it just another attempt by the cosmetics industry to make their products sound more…. scientific?

I also smirked at this entry in their Product FAQ, filed under “What ingredients are in Murine dry&tired:”

pH adjusted for comfort with sodium hydroxide or hyrdrochloric acid.

That just sounds so good.  We won’t even go into the spelling.

The first one is Melvyn Bragg’s “In Our Time” (actually as I write this I realise that these are more radio show than podcast but.. nevermind.  Media convergence etc. etc.).  The programme focuses on ‘the history of ideas’ and the recent Probability – heads or tails? was an excellent introduction to the show for me.  Followed up with a subsequent episode about Lysenko, this has already established itself firmly in my listening schedule.

I was also surprised recently to come across More or Less, a programme which delves into the numbers behind the statistics that we come across every day.  It’s lighthearted and easy going (and unfortunately not currently on air) and is kind of a Freakonomics style look at things.  Very interesting though.

The most recent discovery however was Material World presented by Quentin Cooper.  I’d kind of veered away from pop-sci podcasts (well podcasts in general – I no longer follow the Science, Nature and New Scientist ones), but a section on probability in the most recent episode (largely following the same themes as the Bragg piece) did feature the most amazingly clear explanation of the Monty Hall Problem that I have ever heard, and if the quality is maintained in future episodes as I listen I will be very happy indeed.

Whilst I’m slightly more ambiguous about the ‘saviour siblings’ (a ban on creating them also heavily defeated) I see no real reason to deny people IVF for these kind of medical reasons if you’re going to allow IVF and embryo screening for other people.  I’m just largely against IVF as a means of conception because I am not convinced that couples have any ‘right’ to have children in the first place.

These 2 results however give me great hope that the attempt to lower the abortion time limit from 24 to 20 weeks will also fail.  This particular piece of attempted legislative stupidity (and actually the above 2 as well) flies in the face of all scientific thought, evidence and advice that has been offered.

It still disturbs me greatly that gut feelings, moral panic and general ignorance are allowed to stand against rigorous medical advice and evidence.  I suspect those people who find these things unethical, unacceptable or morally repugnant still consider themselves to be ‘the moral majority’.  I wonder how they feel on days like this when the people they elected to represent them vote in these kind of numbers, and clearly demonstrate that, for now, the moral majority is in favour of allowing science, research and medical breakthroughs to continue.

Various European countries and the academic institutions that make them up already offer compute to scientists at the Grid level – everything from compute clusters for research groups, to the ‘campus grids’.  A step up from this are the NGI (National Grid Initiatives) of which the National Grid Service is the UK’s contribution.  It always surprises me when people get excited about paying for access to commercial services, when free services exist on the doorstep.   Complete with free training.

Now I see that the various European NGIs are looking at ways to support European wide research by coordinating and combining their efforts.  The European Grid Initiative Design Study is currently running and according to its project director looking to make the infrastructure ‘available seamlessly’.  I wonder how much of the ‘cloud computing’ ideal the EGI will take on board.  Anyone who has been on a training course to use these resources currently will know that ease of access probably hasn’t been the watchword in the past, but more of an effort to understand how the various parts of the middleware sit together in order that it can be used at all.

For some reason using the academic infrastructure in place for scientific computing makes more sense to me than going to a commercial concern.  The chances are the NGS et al. are going to be far  more familiar with the challenges of deploying scientific software in Grid environments than Amazon ever will.