I've added a good selection of books to my collection from some of the greatest minds in evolutionary biology. Hopefully they will keep me going for some time and help me not just to further my knowledge of evolution, but to start formulating my own ideas from the often opposing views of these authors!

Let me know what you think of these books, if you have been fortunate enough to read them :-)

We are officially 28 weeks pregnant today. I've been meaning to post about this (the attached pictures) since the 3rd February (which obviously isn't 28 weeks), but I have been too busy with my PhD research.

So, we went to the ante-natal clinic on 27th January 2012, for the so called "anatomy scan", to make sure all the right bits are in all the right places. Everything was fine, fortunately, however, the baby had it's back to us, with both it's arms and legs crossed firmly in place. This had two repurcusions; firstly the sonographer couldn't see all the vessels of the heart properly (although the chambers looked fine) and secondly, we couldn't determine the sex.

This was both a blessing and a curse, as I was in two minds whether I wanted to know the sex or not. We had been able to find out with Ashleigh, our recently turned 3 year old daughter, in fact we had been proactive with that decision, but for some reason I thought it might be nice not to know this time. As a result of not being able to observe the heart properly, we had to make another appointment for a week later.

A week soon passed and we were all back at the hospital (Ashleigh came along too - she is very excited about meeting her "brother or sister" - and we want to keep her as involved with the whole process as we can). The sonographer was able to see the heart more clearly this time, however the baby was in a similar position to that from our previous appointment, and there was no chance of being able to observe the sex. Kelsey, my wife, being rather impatient, decided she would like to know the sex in the moments before the scan, but the sonographer said they wouldn't be able to tell us. I was hoping to get a CD full of pictures from this visit, but that wasn't possible either.

So, I include the two pictures we were able to get of "brother or sister", a.k.a. baby 2.0, from our 27th January visit. You can clearly see the placenta, and the babies face in portrait, along with a portion of the spine and I think some feet curled up towards the placenta... but I guess we'll have to wait to find out the sex, not that it makes any difference to me :-)

This installation was performed on a 2.10GHz Intel Core i3-2310 Asus laptop with 8GB RAM running Windows 7 Ultimate 64bit. I used Strawberry Perl v5.12.3 64bit, MySQL Community Server v5.5.20 64bit and Notepad++ v5.9.8. I also installed GraphViz v2.28.0 for some other packages.

Prerequisites:

Strawberry Perl - http://strawberryperl.com/
Notepad++ - http://notepad-plus-plus.org/
MySQL Server - http://dev.mysql.com/downloads/mysql/
GraphViz - http://www.graphviz.org/Download_windows.php (optional)

Procedure:

1. Install Strawberry Perl, MySQL Server and Notepad++ if you haven't already.
2. Click the start button and type cmd.exe, then right click it and click Run as adminstrator
3. Type perl -MCPAN -e shell and hit enter
4. Type install DBI to install the DBI module, if you haven't already
5. Type get DBD::mysql and hit enter
   
6. Type look DBD::mysql and hit enter
7. Type "C:\Program Files (x86)\Notepad++\notepad++.exe" Makefile.PL and hit enter
8. Search for sprintf, which should take you to line 801 (depending on the DBD::mysql version)
   1. The line has the following code $v = qx( sprintf('%s --user=%s --password=%s version', $mysqladmin , $opt->{'testuser'}, $opt->{'testpassword'}) );
9. You need to remove the qx( immediately in front of the sprintf and the ) just before the semicolon at the end.
   1. The line should now look like this $v = sprintf('%s --user=%s --password=%s version', $mysqladmin , $opt->{'testuser'}, $opt->{'testpassword'});
10. Save the file and return to the command window
11. Type perl Makefile.PL --testhost=localhost --testuser=root --testpassword=yourpassword and hit enter (yourpassword should be replaced with the password you used for the root user when installing MySQL Server)
12. Type C:\strawberry\c\bin\dmake.exe and hit enter
13. Type C:\strawberry\c\bin\dmake.exe test and hit enter
14. Type C:\strawberry\c\bin\dmake.exe install and hit enter
15. Type exit and hit enter
16. You can now try and install (or code) something that depends on DBD::mysql

This installation was performed on a 2.93GHz Intel Core i7 iMac with 8GB RAM running OSX Lion 10.7.3. I used XCode 4.2 build 4D75 and MacPorts 2.0.3. This should also work on earlier XCode versions and/or on OSX 10.5+.

Prerequisites:

XCode - http://developer.apple.com/xcode/ (or from your OSX install disk)
GFortran binaries - http://gcc.gnu.org/wiki/GFortranBinaries
r8s source code - http://loco.biosci.arizona.edu/r8s/

Procedure:

1. Install XCode and GFortran if you haven't already
2. Download r8s (I used version 1.71 from http://loco.biosci.arizona.edu/r8s/r8s1.71.dist.tar.Z)
3. Load the terminal and change to the directory you downloaded r8s to, e.g. Downloads (cd ~/Downloads)
4. uncompress r8s1.71.dist.tar.Z
5. tar -xvf r8s1.71.dist.tar
6. cd r8s1.71
7. You should have four directories (ls -alh) - bin, doc, sample and src
8. cd src
9. nano Makefile (or whatever editor you prefer)
10. Change FC = g77 to FC = gfortran (should be line 5)
11. change LIBS = -lg2c -lm to LIBS = -lgfortran -lm
12. change LPATH = -L/sw/lib to LPATH = -L/usr/local/gfortran/lib
13. make
14. cp r8s ../bin
15. cd ..
16. bin/r8s

Result:

w232-244:r8s1.71 stevemoss$ bin/r8s
r8s version 1.71 (compiled Feb 15 2012)

r8s>

 

Some new books I've added to my collection, thanks to Amazon vouchers I received during the festive season. These will certainly keep me entertained and more importantly, be useful tools for my PhD.

I had a read of http://pathogenomics.bham.ac.uk/blog/2011/08/minimum-requirements-for-a-phd-thesis/ by Mark Pallen recently, on what he discusses are his minimum requirements for examining a PhD thesis, with a particular focus on molecular bacteriology.

I wondered what people might have to add to this? As PhD theses are by necessity variable in content and focus, I'm particularly interested in what you think one should be able to demonstrate as a minimum in your area of expertise!

I'm working on understanding the evolution of the genome with a particular focus on non-coding DNA and gene duplication, utilizing phylogenetic comparative methods and evolutionary bioinformatics approaches, applicable to the study of large-scale genomics data. Any comments relating to these areas would of course be most appreciated and helpful, but I hope that people from a number of different disciplines will comment.

I cross-posted this on the bioinformatics forum BioStar http://biostar.stackexchange.com/questions/16258/what-are-your-requirements-when-examining-a-bioinformatics-related-phd-thesis and would welcome your thoughts there, if applicable, as well as here!

I'll update this post with consensus thoughts as the coments acrue.

I've uploaded the latest QIIME release, version 1.4.0, which has various fixes and updates, to BioTorrents and am currently seeding it. The more people that download it and seed it, the better. The download rate, for me at least, from the QIIME team's Colorado server, was particularly slow. Hopefully getting more people seeding on BioTorrent will take the pressure off their server, whilst also speeding up the download overall!?

You can retrieve the torrent here - http://www.biotorrents.net/details.php?id=262

Update: I also added it here http://burnbit.com/torrent/183016/QIIME_1_4_0_amd64_vdi_gz

My supervisor at university is an avid Mekentosj Papers fan. One of the issues with Papers however, is the lack of a central shared media resource for synchronisation across multiple machines. You can synchronise to the iOS version of the app using WiFi, if you are on the same network, but this is one of the real limitations of the software in general.

This is where Dropbox (or other such software) comes in handy. You can move your Papers library to a Dropbox folder and automatically synchronise your database across devices. However, if you have a copy of Papers open when using another copy, in another location, it can create database conflicts, as Papers locks the database file for writing when it is open. If you have Papers running at work and at home, and forget to close it before you leave the office on an evening, or leave home in the morning, for example, then this can cause annoying problems.

The solution is a crontab job (which thankfully, as Papers is Mac only, it doesn't matter that cron isn't supported in Windows)!

The preferred method on Mac is to use launchd (http://developer.apple.com/library/mac/#documentation/Darwin/Reference/ManPages/man8/launchd.8.html), but cron is still supported.

I coded a kill_papers.py script in Python. It needs to run as root in crontab (http://unixhelp.ed.ac.uk/CGI/man-cgi?crontab). I have created a crontab line in the kill_papers.cron file that causes the Python script to run as root at 18:30 every day and the script itself sends a SIGTERM signal, asking the program to quit gracefully (as opposed to SIGKILL, SIGINT or SIGSTOP). It should work for Papers and Papers2 (I tested it with both running on OSX 10.7). Of course you can edit the cron file to run at a different time, in the morning for example, on your home machine.

You will need to download and install the Python module psutil-0.4.1 (from source code) first (http://code.google.com/p/psutil/).

1. Download using:
   1. http://code.google.com/p/psutil/downloads/detail?name=psutil-0.4.1.tar.gz&can=2&q=
2. Extract from terminal using:
   1. cd ~/Downloads
   2. tar -zxvf psutil-0.4.1.tar.gz
3. Install using:
   1. cd psutil-0.4.1
   2. sudo python setup.py install

To install you should do the following from the terminal (assuming you have downloaded the files to your Downloads directory):

1. sudo cp ~/Downloads/kill_papers.py /usr/sbin
2. sudo chown root:wheel /usr/sbin/kill_papers.py
3. sudo crontab < ~/Downloads/kill_papers.cron
4. sudo crontab -l

This does the following:

1. Copies the kill_papers.py script to /usr/sbin using sudo (required as the destination directory is owned by root)
2. Sets ownership of the file to the root user and wheel (sudo users) group so that cron can run it properly
3. Copies the line from kill_papers.cron into root's crontab file (sudo is required to edit root's crontab file)
4. Displays root's crontab list (with a lowercase L not an uppercase i), which should give us:
   1. 30    18    *    *    *    root    /usr/bin/python /usr/sbin/kill_papers.py

Alternatively you could run sudo crontab -e (sudo allows us to edit root's cron file) and add the line from the cron file to that window. The editor is vi so you'll need to know the basics of vi to get around that (http://unixhelp.ed.ac.uk/vi/).

Let me know if this works for you, and if not, if you have any problems :)

I spent some time toying around with the title to this post, trying to think of something snappy, a spin on words, or perhaps something a little cryptic, but finally settled on something simple and to the point... I'm going to be a daddy again :)

We've known since October 2nd, or rather Kelsey has and I've known since October 3rd, my birthday, when Kelsey wrapped up her pregnancy test as a birthday present for me (I'm not squeamish). We've had a couple of scans since, one on November 4th and the most recent today, November 28th. I have attached the scan pictures to this post.

We're due on 8th June 2012, so are 12 weeks and 3 days today. Ashleigh, our 33 month old has come with us to both scans and has been very excited at the prospect of having a "brother or sister" as she keeps saying. She keeps kissing and cuddling Kelsey's belly and has even decided on names for us already (although, at Kelsey's request, I'll be keeping those ones secret). She is great with babies too, always helping out with the younger ones at nursery, so I'm sure she will be an excellent sister and really help us out.

I'm really excited about becoming a Dad again too. I was a little apprehensive when discussing it previously, as my love for Ashleigh is so intense, that I was both worried that I couldn't love anything else as much, or that my love for Ashleigh may somehow suffer. Of course, this is unwarranted anxiety and surely has also been experienced by every parent who has had more than one child! It will be amazing to have another beautiful child to share my life with, to teach them the beauty in this world, and of course as a companion sibling for Ashleigh.

The fact that I am into the second year of my PhD has played on my mind - I have a heavy workload as I'm sure all doctoral research students can attest to, but I am highly motivated, focused and seem able to maintain a healthy work-life balance, so I can't see it being too much of an issue. I am of the opinion that things like this are difficult to plan for ideal points in one's career (although the due date coincides nicely with the start of Kelsey's summer break from university) and that often it is just best to go with the flow - as seems to be a large part of my philosophy on life in general.

So, I'll keep you up-to-date on any occurrences, both baby and PhD, whilst I wish my life away looking forward to meeting the new addition to my family :-D

So, the browser stats show that Firefox's dominant hold on the market for the last few years is being gradually encroached on by Google's Chrome. I had been using Firefox since it's first release back in November 2004, until earlier this year, when I started having problems with memory usage and overall performance. I wondered if this might be down to my Zotero library plugin and del.ici.ous bookmark toolbar, so went as far as disabling them, and other add-ons to try and improve performance. At the time Google Chrome was gaining more media coverage and I had been using it on and off since late 2010, so decided to switch to it as my main browser.

I had been quite happy with the switch and the excellent number of extensions that were available, that seemed to have little impact on performance or memory usage, but for that last few releases and over the last few months I have begun to notice issues with Chrome too. I have experienced hanging, memory issues and even on occasion, a complete refusal to load pages, that has required a browser restart. These issues resulted in my swapping back and forth between Firefox and Chrome to assess the best performance. My PhD supervisor also commented on these issues, which he believed to coincide with interface updates to Google's cloud pages, e.g. Google Docs and of course the recent release of Google+. Whether this is coincidence or not, I have sometimes noticed improvements when closing down Google related tabs.

With the Firefox memory issues starting to gain press coverage, it seems they have taken things quite seriously and although they have switched to a fast release cycle, they have also been monitoring and improving memory usage and performance over the last few releases. Now at version 8, the browsers seems to be moving back in the right direction and I'm happy to say that I have reverted completely back to using it as my default browser on both Windows, Linux and my Android phone. An iOS release for my iPad wouldn't go-a-miss, but I'm not sure how well Apple would respond to an App Store submission of that sort.

I'm hoping that the future versions of Firefox will see continuing improvements and hopefully a return to their former glory. I feel however, it will be difficult for any browser in the market to gain as much popularity, or should I say usage, as Internet Explorer did in it's early years.

Get Firefox here now - http://www.mozilla.org/en-US/firefox/all.html