qPCR
January 12, 2011 by Steve · 2 Comments
After having a look around at the available instruments for qPCR the lab has invested in a Qiagen Rotor Gene Q. This should enable me to do accurate quantification of mRNA from the gene circuit without having to do northern blotting. I am hoping it will fast forward the data generation to move into modelling. Training is booked in for tomorrow, so we will see what it can do…
Mint 10
November 13, 2010 by Steve · Leave a Comment
I have made some adjustments to this “article” I wrote after a particularly venomous email from tlaid@hotmail.com. I would have been happy to edit the “article”, credit the sender, and thereby correct the details that had caused a great deal of outrage, however nothing so constructive was provided. I hope the ammended version is more acceptable.
Linux Mint 10 (“Julia”) has been released, based on Ubuntu 10.10 (“Maverick Meerkat”). I’ve been running Ubuntu for about 4 years now and for the past couple of years have been running the spin off distribution “Mint“. Linux Mint is composed of many software packages, of which the vast majority are distributed under a free software license (also known as open source). The main license used is the GNU General Public License (GNU GPL) which, along with the GNU Lesser General Public License (GNU LGPL), explicitly declares that users are free to run, copy, distribute, study, change, develop and improve the software. Linux Mint also includes some proprietary software, such as the Adobe Flash plugin, and uses a Linux kernel that contains binary blobs. Linux Mint is funded by its community of users. Individual users and companies using the operating system act as donors, sponsors and partnersof the distribution. The financial support from the community and advertising on the website helps to keep Linux Mint free and open source [taken from wikipedia].
Many hardened linux users can’t stand the site of Ubuntu as it moves more into the Windows world of armchair computing and presents users with a computer they again don’t need to understand the workings of. I’ve flirted with Mandriva, Arch, Fedora, Suse, and Slackware but keep coming back to Ubuntu just for the ease of setup and the canonical repositories. At the moment I often just don’t have the time to go through some of the problems encountered when compiling from source code and hunting down dependencies. This isn’t a distrubution or OS fault – it’s just I don’t have enough understanding to race off and sort everything out, and I don’t have the time to learn more at the moment.
For those who don’t have enough experience of the command line and inner working of their computer, Linux Mint offers an even easier solution than Ubuntu with a nicely tweaked GUI to boot. Mint also has some nice extras of it’s own like Mint menu that puts all your most used applications on the start menu for you like Windows 7. Mint backup also provides archiving and imaging of your OS for when you inevitably break it.
Mint is beginning to move into a debian based distribution and moving away from Canonical. The plans to move Ubuntu to the Unity desktop on Wayland will also push Mint further away from Ubuntu as Mint plans to retain the XServer, so time will tell as to whether Mint stands up on its own. Personally, if I make the move to debian I could be tempted at #Crunchbang’s “Statler” distrubution with XFCE as this lean OS is fast. A rolling distribution of Mint under Debian however could be a good move as, personally I don’t like the 6 month distrubution upgrades. This is what tempted me to Arch, but the lack of canonical repositories drew me back to Mint. I just wanted to get stuff done, and I just couldn’t do it in Arch with my current kung fu level! A rolling debian Mint with the repositories and tweaked interface however could be somewhat tempting. sudo apt-get update && sudo apt-get upgrade is far less painful than fdisk. Also, the potential lack of compatibility between wayland and older xserver applications could mean Ubuntu becomes increasingly incompatible with other linux apps and presents a problem with upgrading and backwards compatiliblity. Conversely, it will also drive forward the implementation of Wayland which might be very good for Linux’ ageing and bloated xserver. It will be interesting to see if Ubuntu becomes a future Apple and splits away from linux like OSX did from BSD, evolving into its own OS or whether it will be a spearhead for the next generation of Linux OS.
So, if you fancy a dip into the world of Linux and want something easy to get you going then take a look at Mint sometime. I plan to drop the training wheels one day, but for now it lets me peddle along and enjoy the scenery. Mint comes with seperate downloads for gnome, KDE, and Fluxbox desktops as well as the debian based build. There are small CD releases with the base install and DVD ISO’s with all the extras.
There is also a much more informed account of Mint’s development over on wikipedia if you want more information.
one small step for your PI, one giant leap for you
November 9, 2010 by Steve · Leave a Comment
The lab has moved to it’s new home at University of Warwick. After a few months of packing, unpacking, packing, unpacking, packing again, and then unpacking, our stuff is out on the benches and the lab is starting to function. The project can continue after 3 months of effective down time. How this will effect the final year of this work I have no idea yet. I was behind before I started and I wonder if I’ve already reached critical mass anyway.
The new lab is functional. Not quite the state of the art MIB but the necessary facilities are available. The University has a different culture to Manchester and will require some acclimatization. The University is undergoing some “restructuring” in these “hard economic times”, and it’s not hard to see the University is somewhat financially challenged.
On the upside we have a nanodrop (don’t leave your lab without one!) and in a rather unexpected turn of events we can invest in a qPCR machine. I have been investigating the Roche Lightcycle 480, Applied Biosystems StepOne and a BioRad module for our c1000 thermal cycler. The Roche machine doesn’t need a ROX standard for normalizing the signal from the heating block and is interchangeable between 96 and 384 well configurations. Separate filter sets for the laser also gives some future proofing and flexibility. Will see what the StepOne looks like later this week.
On a lighter note, my colleague Natalie Stanford over at PhD Fodder.co.uk posted this hilarious article about Anatidaephobia – the fear of being watched by a duck. An epic fail for the site’s advertising robot. Anatidaephobia is a worrying condition on a campus that boasts in the prospectus of having more ducks than students. Who’s watching who’s watching who?
Copasi update to build 33
October 7, 2010 by Steve · Leave a Comment
Copasi build 33 has just been released. Download it here.
Version 4.6.33 (development)
Release Date: October 7, 2010
New Features since COPASI 4.6 (Build 32)
* Graphical User Interface (CopasiUI)
o Notes in text or XHTML format are now available for compartments, species, reactions, global quantities, events, and kinetic functions.
o Support links in XHTML notes.
o Support of render informations in graphical model layouts.
* Simulation Engine
o Enhanced MCA algorithm performance by applying a new selection criterion before each internal step.
o Added an stochastic algorithm (Adaptive SSA/Tau-Leap) which dynamically partitions the model into parts simulated by the direct algorithm and the Tau-Leap algorithm.
* SBML
o Import SBML Level 3 Version 1.
o Added SBML notes support for compartments, species, reactions, global quantities, events, and kinetic functions.
o Added MIRIAM annotation support for events.
o Support for the SBML Render Extension.
Bug Fixes since COPASI 4.6 (Build 32)
* Graphical User Interface (CopasiUI)
o The selected items in the navigation tree do now correspond to the object displayed in the main widget.
o Fixed a crash caused by not marking any of the check boxes before, during, and after in the plot definition widget.
o Fixed progress report for the scan task which was not updated during the execution.
o Fixed crash which could occur in a model with circular calculation dependencies which additionally used sliders.
o The delete buttons in the tables are now only active when one or more objects are selected.
o In the steady-state result widget the button to update the model is now working.
o Fixed crash which occasionally occurred when saving the ODEs in TeX format.
o Fixed crash caused by saving a model where reports referenced in tasks have been deleted by the user.
o Enabled scrolling for the rendered mathematical expressions.
* Simulation Engine
o Fixed problem in Stochastic Gibson Bruck algorithm which could make COPASI unresponsive.
o Fixed problem in the MCA task which did not execute the selected sub task when the model was created with a previous version of COPASI.
o Fixed crash which occasionally occurred when exporting the ODEs to C.
back home
September 20, 2010 by Steve · Leave a Comment
Back in Manchester after a 20 hour marathon across Europe from Spetses, and working through the depression of leaving a Greek island for cold, damp England. Many things to do now that the final year has arrived. Spetses conference was useful in providing some contacts that can provide additional yeast strains for me to work with and some important changes I can make to the modelling side of my project. Much thanks must go to the biochemical society for providing the travel and conference funds that it possible to attend.
I will change my modelling from mass action kinetics to more michaelis menten style with hill coefficients. Mass action kinetics can’t saturate but at some point the transcription and translation reactions will. The DNA and mRNA transcripts will at some point max out the number of polymerase and ribosome molecules. I can also incorporate expressions for activation and inhibition which will be important to model correctly in order to simulate the feed forward loop. The equations will be derived from Professor Pedro Mendes’ 2003 paper.
Final lecture
September 17, 2010 by Steve · Leave a Comment
Quick swim then back for final lecture from yoshi nakamura of tokyo. RNA bio mimicry for designing therapeutic drugs from aptamers. Interesting animal model results for treating auto immune disease. Some cash issues for scale up to kg of rna however.
September 17, 2010 by Steve · Leave a Comment
Igem workshop this morning. We had 2 hours to work up a biological engineering project from concept to project proposal. Many fun ideas were presented. Good team working exercise. Later phil hollinger presented his work on protein evolution. Interesting research on possible origin of self replicating molecules. Moved onto synthetic information carrying molecules and potential routes for building orthogonal circuits.
September 17, 2010 by Steve · Leave a Comment
Drew endy dropped in to talk about standardizing components for bio engineering, and characterizing interacting the individual parts. Professors Freemon and Kitney from imperial collage london talked about modeling of biological modules and their efforts to standardize construction.
Day 3
September 14, 2010 by Steve · Leave a Comment
Day 3. Jean Beggs quantitative analysis of rna processing then copasi workshop. Interesting combination of lab observation and stochastic modelling. Potential splicing surveilance factors was intriguing. Intro to copasi modelling next so a practical exercise. Excursion this afternoon. Weather improved. Sun tan 4 all. Tutorial group dinner tonight.
Spetses 2010
September 13, 2010 by Steve · Leave a Comment
Febs 2010 conference day 2. I have got my ageing nokia e65 connected via wireless and can make some basic blog postings throughout the conference. Content will be limited by flaky signal and flaky phone!
Yesterday Tom Blundell gave an enthusiastic talk on drug discovery, and it’s potential to generate financial as well as scientific hits. Today Tobias van der Har talked about measuring gene expression rates followed by Pedro Mendes on modelling bio chemical networks. The afternoons form tutorial sessions with the speakers which is a good opportunity to chat to senior researchers in the informal setting: ‘beach’ 
i have met some students from imperial collage doing similar work with the igem projects. The weather and location is excellent and helps students mix and exchange cultures as well as science.