But maybe the Dundee server is down. Or maybe you think your local machine will do things faster. Or maybe you work on über secret sequences in some Faraday cage bunker with no permanent network connection. In each of these cases, you may want to run your own local JABAWS server and use that instead. In this case, read on.

Download the JABAWS war file (direct link here).

Install Apache Tomcat and the management interface:

sudo apt-get install tomcat6 tomcat6-admin

As root, edit the /etc/tomcat6/tomcat-users.xml file to enable admin access.

Between the <tomcat-users></tomcat-users> tags, add:

<role rolename="admin"/>
<user username="tomcat" password="s3cret" roles="admin"/>

where ‘s3cret’ is a secret password for the user ‘admin’.

Go to http://localhost:8080/manager/html/ and login as ‘admin’ and the password you set.

Under “WAR file to deploy”, click on the “Choose File” button, and select the jaba.war file you downloaded.

Now you need to set the permissions of the Muscle/Mafft/Clustal etc binaries that come packaged with JABAWS. Type the following commands:

cd /var/lib/tomcat6/webapps/jaba/binaries/src

sudo chmod +x setexecflag.sh

sudo ./setexecflag.sh

This should do it .. in Jalview, go to Preferences, and under the “Web Services” tab add a new service URL “http://localhost:8080/jaba” (no quotes, no trailing backslash).  Now when you load an alignment, your local JABAWS server should appear under the “Web Service->JABAWS Alignment menu”.

For the record .. I tried this under the version of Jetty packaged with Ubuntu 11.04, but I couldn’t get it to work so I gave up and just did it with Tomcat as per the JABAWS documentation.

Links:

This HOWTO is an Ubuntu specific regurgitation of the docs below.

http://www.compbio.dundee.ac.uk/jabaws/manual_qs_war.html

https://help.ubuntu.com/10.04/serverguide/C/tomcat.html

http://www.flickr.com/photos/alicebartlett/ / CC BY-NC 2.0

• MajorGroove.org pitches itself as a ‘forum for biologists’, which it is, however most of the content currently focuses on X-ray crystallography and associated techniques. It is currently in ‘bootstrap mode’, which means that reputation requirements are a little less strict until the userbase and site activity has grown to a critical size. Is there even a need for a Stack Exchange forum for biological crystallography ? Macromolecular crystallography already has a single, central, de facto standard forum – the CCP4BB mailing list. While it may be antiquated by Web2.0 standards, CCP4BB works well for a lot of people, and there is a huge amount of useful and important information buried in it’s archives. For many crystallographers, it seems CCP4BB would only be extracted from their “cold dead hands”. Despite this, I think the Stack Overflow format will be very beneficial for people new to the field.  As a side note - I discovered MajorGroove via Graeme Winters XIA2 blog right around the time when I was considering kickstarting a “Stack Overflow for crystallography”. At the moment it seems that a small userbase of crystallographers is already established on MajorGroove and there would be no purpose for another near identical forum. Even if questions about other techniques in the biosciences start to dilute out the structural biology, one click on the ‘crystallography‘ tag or the ‘ccp4‘ tag, and you can get straight to the good stuff. (In fact this feature was deemed useful enough by Google that they decided to bless the ‘android‘ tag on Stack Overflow as the official Android Q&A forum).
• NMRWiki Q&A (http://qa.nmrwiki.org/) is a StackExchange-clone for magnetic resonances, mostly focused on NMR, but also open to EPR/ESR and MRI users. It’s not actually running on the StackExchange platform, but uses the open source OSQA / CNPROG clone, built on top of Django. As far as I know, there is no “CCP4BB for NMR”, which makes the NMRWiki Q&A site potentially even more valuable to structural biologists than it’s crystallography centric cousin, MajorGroove. Back when I was doing my PhD using protein NMR spectroscopy as my primary technique, there were very few good resources like this online – I do less NMR these days, but you can bet that I’ll be using the NMRWiki Q&A and it’s associated wiki to refresh my memory and catch up on need methodological developments in the future.
• BioStar (http://biostar.stackexchange.com/), a StackExchange for bioinformatics, computational genomics and systems biology questions and answers. This one is busier and better established than the above mentioned forums, probably by virtue of the fact the bioinformaticians spend more time in front of the computer than your average molecular biologist or structural biologist.
• And, for a bit of fun: Skeptic Exchange (http://exchange.bristolskeptics.co.uk/), which covers rational questions and answers to various topics including pseudoscience, faith healing, the supernatural and alternative medicine.

Want more ? There are a bunch of science related StackExchanges listed under “Science” here: http://meta.stackexchange.com/questions/4/list-of-stackexchange-sites .. and digging back through the FriendFeed archives I see Matt Todd initiated a concise listing (which if I’d seen, I probably never would have started this post).

And now, the latest* news Stack Exchange 2.0 will be ‘free‘. It looks like they are trying to structure the new Stack Exchange ecosystem a bit like the Usenet hierarchy (comp.*, rec.* etc), with a fairly involved discussion, proposal and acceptance process for new sites – it’s unclear yet whether this approach is going to work out better than just open sourcing the whole shebang, but time will tell. My guess is that BioStar, MajorGroove and probably even an incarnation of NMRWiki Q&A will eventually become part of this formalized ecosystem.

On one hand making StackExchange sites free to run is great – it lowers the barrier to entry to allow many more sites to emerge and operate. On the other hand, as we have seen with the acquisition of FriendFeed by Facebook, not having a clear revenue stream can ultimately leave communities  (such as The Life Scientists) without any certainty in a sites future, potentially impacting growth and participation. Personally I’m much more inclined to invest time in a site if it is something like Wikipedia, where I know my contributions are very likely to live on, in some form, for decades (centuries ?) to come. Ideally the archives of these new Stack Exchange sites could become useful online resources for decades to come – but with a single company at the helm and a “Web 2.0 business model”, continued operation for even a decade seems unlikely. The one saving grace: all content on the new Stack Exchange sites will be licensed under a Creative Commons license – so if Stack Exchange itself is acquired and shut down, we will always be able to preemptively leech the archives and provide them online elsewhere. Maybe it’s strange that I’m already thinking about archiving the new Stack Exchange upon it’s demise before it’s even begun, but I think it’s important to take the long term view with our data and recorded wisdom. Unlike when in 1994 when GeoCities (R.I.P) was started, teh Internets is no longer a fad – the hard disks connected to it are fast becoming the sum of all accessible human knowledge, so we’d better make sure we can retain the good bits for a little longer than 10 years.

* – as all too common these days .. I’m a little behind the curve on this one. I meant to finish this post a month ago, but with a busy time pre-holiday, then the actual holiday, a month has gone by.

It barely warrants it’s own blog post, but here we go anyhow: my one-liner shell script for counting the number of sequences in a FASTA “flat-file database”, based on the presence of the “>” header symbol.

Dead easy huh ? I put this in ~/bin/countseqs, make it executable (chmod +x ~/bin/countseqs) and use it in lots of situations, as a quick sanity check.

(oh, btw, this is not public domain and u can’t use it for commercial gain without paying me a license fee. academic users can fax me something for a free license. k thx bye).

Couldn’t help myself … everyone else is doing it

Recently I needed to install NCBI wwwblast on my local workstation to enable some software that needed to interface with BLAST via the web service. It was straightforward to install, but I took some notes, because there were a few changes required with respect to the official wwwblast documentation at NCBI. These instructions are for Ubuntu 8.04, but probably will work with many recent flavours of Debian.

Download and install

Download NCBI wwwblast from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/ (The version I used was wwwblast-2.2.18-ia32-linux.tar.gz).

Untar it into /var/www/ , preserving permissions.

$ cd /var/www/

$ sudo tar zxvpf wwwblast-2.2.18-ia32-linux.tar.gz

You will also need to make sure csh (the “C-shell”) is installed, since the blast.cgi script needs this to run:

$ sudo apt-get install csh

(Thanks to jpopesku for spotting this missing package [comments below])

Set up Apache2

The instructions in the official wwwblast manual didn’t seem to work for Apache2 .. (could be a typo: Follow SymLinks should be FollowSymLinks … one camel-case word without the space). I put this in into the VirtualHost definition in the standard /etc/apache2/sites-available/default file used by Apache2 in Ubuntu 8.04.

The code above was inserted just before the </VirtualHost> closing tag.

Restart Apache for good measure.

$ sudo /etc/init.d/apache2 restart

Configure your wwwblast to see your databases

Assuming you already have some existing BLAST formatted databases made with formatdb, you will then need to configure wwwblast to find them, as per the manual. In short, this involves putting the BLAST database files into /var/www/blast/db/ (or symlinking to the files), modifying /var/www/blast/blast.rc (or one of the other *.rc files, for other BLAST programs, eg psiblast) to associate the database name with a BLAST program, and modifying the dropdown database list in /var/www/blast/blast.html (or one of the other *.html files for other BLAST programs) to add the name of the database(s).

My BLAST databases live in /data/databases/blast/, so I simply moved the example database directory /var/www/blast/db to /var/www/blast/db.orig:

$ sudo mv  /var/www/blast/db /var/www/blast/db.orig

then symlinked /var/www/blast/db to /data/databases/blast:

$ sudo ln -s /data/databases/blast /var/www/blast/db

In /var/www/blast/blast.rc I changed the line:

blastp test_aa_db

to:

blastp nr swissprot pdbaa

(you may also want to configure blastn etc in the same way)

In /var/www/blast/blast.html, I changed the test database code:

to:

(you may want to do this for other BLAST programs too, eg also edit psiblast.html)

This will allow be to search the nr, swissprot and pdbaa databases I have installed using plain-vanilla BLAST.

Test it out

Go to http://localhost/blast/blast.html.

You should find the wwwblast interface, with a dropdown box featuring the database(s) you added. Run a test search with your favorite sequences (ensure you also select the correct blast program, eg blastp !). Enjoy using your own CPU time !

I recently needed to make a simple, two dimensional figure of a beta-barrel membrane protein. I went hunting for programs that might take a sequence and/or structure and produce a pretty looking diagram to save me constructing everything by hand. Here are two I found and tried.

TMRPres2D

Ioannis C. Spyropoulos, Theodore D. Liakopoulos, Pantelis G. Bagos and Stavros J. Hamodrakas TMRPres2D: high quality visual representation of transmembrane protein models Bioinformatics. 2004; 20: 3258-3260. (link)

Pros:

• Cross-platform (Java)
• Simple interface, GUI (zero learning curve)
• Lots of input options (defines transmembrane regions directly from SwissProt or PIR annotations online, takes input from several transmembrane region predictors)
• Lots of output formats and options (Postscript, gif, jpg, png, svg, bmp)
• Various colouring options (hydrophobicity, charge, “printer friendly”)
• Makes reasonable looking diagrams of helical transmembrane proteins

Cons:

• Doesn’t handle beta-barrel membrane proteins gracefully (strand drawing is overlapped, messy).
• The membrane is assumed to be a eukaryotic plasma membrane, with labels “cytoplasmic/extracellular” (which should be, for instance, “extracellular/periplasm” for a bacterial outer membrane protein). This is easily changed on the diagram with external editing.

TeXtopo

Beitz, E. (2000), TeXtopo: shaded membrane protein topology plots in LaTeX2e. Bioinformatics 16: 1050-1051. (link). See the original publication or Professor Eric Beitz’s site for a better example than my image.

Pros:

• Beautiful, clean, publication quality diagrams, courtesy of LaTeX
• Multiple input options (Swissprot format, PHD, HMMTOP, user defined)
• Multiple sequence annotation options including colouring by various physiochemical properties (hydrophobicity, charge), sequence conservation or user defined schemes.
• Will depict membrane embedded half-loops and lipid anchors.
• Versatile output (Postscript, pdf, dvi, basically anything that LaTex can be rendered as)
• Also can generate attractive looking helical wheel plots
• Did I mention the output is clean and looks great … ?

Cons:

• Steep learning curve for the uninitiated, despite extensive documentation (ie LaTeX code, no GUI)
• No support for beta-barrel membrane proteins

If I ever need to make a 2D diagram of a helical membrane protein for a publication, TeXtopo would be my first choice. For quickly getting an overview of some transmembrane prediction results or a protein with defined tranmembrane regions in Uniprot, TMRPres2D is the quickest and easiest method.

In the end, since neither program would do a decent job at cleanly depicting the strands of a beta-barrel in a simple 2D plot, I ended up coding my own hackish solution (svg_barrel.tar.gz or svg_barrel_gui_win32.zip) using Python and a tweaked version of SVGdraw.py. This allowed me to generate some SVG graphics to use as a starting point, and then hand edit the result in Inkscape to align strands to loosely match the real hydrogen bonding patterns. I also added some simple beizer curves for the loops, since neat placement of loop residues was the tricky part that I decided I didn’t have time to tackle.

Here’s the end result, after hand editing:

And here is the 3D version, as a point of reference:

The 2D vector diagram could do with some work to aid in a more accurate representation (unfortunately ‘flat’ views of a 3D barrel always have to make some compromises), but it does the job. The goal was to keep it simple … simple it is. One day I may extend this code to actually use known structure coordinates to automatically align the strands (saving tedious manual alignment), and write some code that properly lays out the loops.

Anyone know any other programs of similar functionality I’ve missed ?

Here’s a screenshot of Qutemol running under Cedega on Ubuntu Gutsy Gibbon, just to prove it.

No, it’s not Photoshopped … (or GIMPed) …

I’ve just installed it on Ubuntu Feisty Fawn from the Google Linux software repositories, and while it’s currently only indexed about 1 % of my files, my initial tests suggest it is pretty slick … a quick Ctrl-Ctrl, and up pops the search box. Apart from all the things I’d expect, like indexing the content of pdf files, directories like “/usr/man” are included on the default path list, so I presume it also looks inside man pages. One problem I’ve noticed so far in my very quick testing is that it seems to not follow symlinks to directories and won’t let me add them as paths to index. The effect is that my “/home/perry/documents”, which is actually a symlink to a larger partition, does not get indexed unless I add it to the path list with it’s real path.

While there are already similar offerings for Gnome (eg Beagle) and KDE (eg Kat), my gut feeling is that Google Desktop will be my preferred option for the moment. Maybe one day we will get lucky, and Google will even make it FOSS (not holding my breath though).

Here’s how I installed it on Ubuntu Dapper (the package is for Debian Sarge, but seems to work fine):

Download flashplugin-nonfree.

Use right-click, “Save Link As …” and save it to \tmp.

$ cd /tmp

$ sudo dpkg -i flashplugin-nonfree_9.0.21.78.4~bpo1_i386.deb

(you’ll be prompted for your password, and once you provide it, the install should happen)

You can check if it worked by typing about:plugins into the URL box in Firefox. You should see something like “Shockwave Flash 9.0 d78″ on that page.

Now go view some F-F-F-Flash cartoons (I don’t think Homerstarrunner requires Flash 9, but it’s the only Flash site I use on any regular basis)

For drafting manuscripts of scientific papers, pictures/photos/illustrations etc are usually referred to as “Figures”, however when inserting a picture via “Insert -> Picture -> From File ..” the default behavior of OpenOffice is to use the caption “Illustration”. This will not do.

From the OpenOffice Writer Guide, Chapter 8 [pdf], here is how to get it to use “Figure” by default:

• Open the “Tools -> Options –> OpenOffice.org Writer—> AutoCaption” dialog box.

• Under “Add captions automatically when inserting section“, check
OpenOffice.org Writer Picture, and make sure its checkbox is ticked.

• Under the Category drop-down list, enter the name that you want added,
eg, Figure, in the place by overwriting any sequence name in the list (it will probably have “Illustration”, before you overwrite it.) I also like my Figure label bold, so I also selected “Strong Emphasis” from the “Character Style” dropdown box. Press OK to save the changes.

Now you can insert a Picture using “Insert -> Picture -> From File ..” and the label should be “Figure”, not “Illustration”. The picture comes in its own frame, and you can edit the figure legend directly in the document.

Hmmm … Latex is not looking so bad again ….