OfficeTab
October 13, 2009 by Steve · Leave a Comment
Useful tool of the week: OfficeTab
OfficeTab adds a tabbed interface to Word, Excel, and Powerpoint. Rather than having separate windows with different files, this little 3rd party Office add-in opens them as tabs within the main application making it much easier to flick between different windows. The authors site is in Chinese but the download links are in English.
September 21, 2009 by Steve · Leave a Comment
Today is 25 years of David Braben and Ian Bell’s Elite video game. This isn’t really systems or synthetic biology, but back in 1984 it was the inspiration of Cambridge students David Braben and Ian Bell that captured the imagination of a generation who spent the next 25 years carving a name for themselves in the Elite universe. Published by AcornSoft in September 1984, Elite has long been considered one of the best video games of all time and inspired the whole “space trading” gaming genre with games such as Eve online, Freelancer, and the X series continuing the tradition. Elite was the first video game to create an “open universe” for players to explore and follow their own path as they chose, creating the concept of “sandbox” gaming popularized by the likes of Grand Theft Auto and Morrowind decades later. Long before the “RPG” scene emerged from dungeons and dragons with class based character development Elite enabled players to choose their own path as explorer, trader, pirate, bounty hunter, mercenary pilot, or all of the above literally doing as they pleased within a dynamic universe. Players could upgrade their ships to haul more cargo across the galaxy or more effectively vaporize the competition on their quest for “Elite” combat status. Explorers could roam over 2000 worlds across 8 galaxies, while budding entrepreneurs could chose to find lucrative trade lanes between planets trading between industrial and agricultural economies slowly making their fortune. Meanwhile more nefarious players could become bandits and pirates, stalking rich systems for cargo laden traders, living as a fugitive from deadly Viper police patrols, seeking refuge in anarchic systems dealing in contraband narcotics and slaves. Whatever your persuasion, Elite had a corner of the galaxy for you.
Many of the aspects of Elite sound routine in 2009, with the likes of Eve online, World of Warcraft, and Starwars Galaxies, but all this was available 25 years ago on an 8bit home computer with 32kb of memory and no internet and was an enormous computing achievement. Elite contained 8 galaxies, each with 256 planets which had to be procedurally generated. A single seed number was run through a fixed algorithm the appropriate number of times and created a sequence of numbers determining each planet’s complete composition (position in the galaxy, prices of commodities, and even name and local details — text strings are chosen numerically from a lookup table and assembled to produce unique descriptions for each planet). This means that no extra memory is needed to store the characteristics of each planet, yet each is unique and has fixed properties. Each galaxy is also procedurally generated from the first. Elite was a technical masterpiece of it’s time and remains unbeaten in it’s achievements and success.
For those who have never experienced the Elite way of life check out the 25th Anniversary website, or for those who fancy dusting off their old combat skills Oolite continues the legacy of Elite with community maintained content and development
… at least while a generation awaits Elite IV.
COPASI – Complex Pathway Simulator
September 9, 2009 by Steve · Leave a Comment
A few weeks ago I attended a modelling and simulation Copasi workshop run at the MIB by Professor Pedro Mendes. I had attempted to blog about it previously but lab work got in the way.
The workshop was a 3 day event detailing all aspects of the Copasi software, much of which can be found in chapter 2 of the “methods in molecular biology” (2009) Volume 500. 1-43, available as a preview here. (There is also a publication associated with Copasi by Hoops et al. (2006) Bioinformatics 22, 3067-74). I’m no mathematician, so my description of Copasi wont be the most accurate! For me, Copasi is a graphical user interface into the world of mathematical modelling providing an immediate step up in to the capabilities of Matlab and Mathematica armed scientists without requiring particularly large amounts of experience of programming or modelling. The software forms a fundamental toolkit of everything a biologist, or mathematician/computer scientist, needs to build models of systems of reactions and run simulations on them. You can enter your reactions using symbolic algebra equations such as those found in many standard biochemistry textbooks, or directly as systems of ODE’s so it is familiar to both wet and dry scientists. A large number of standard enzyme kinetics equations are available when creating your model such as Michaelies Menten types and hill equations as well as all kinds of inhibitor-substrate relationships, and the ability to enter your own.
At its most basic you can input reactions between species of compounds using symbolic algebra and then create plots of the behaviour or those species as they react together in your system over time. You can quickly gain a grasp however of the underlying power of Copasi when you begin to make more sophisticated enquiries of your system. Using the graphical interface you are able to perform a range of systems biology / modelling techniques from finding steady states, to metabolic control and sensitivity analysis. The real power behind Copasi comes from the advanced features however, particularly the parameter scan which is currently not available in any of the equivalent simulation tools and would require substantial programming experience in Matlab or Mathematica. The parameter scan enables you to set a certain parameter at a range of values and repeatedly run the simulation, plotting the output from each iteration. This, for me was a hugely powerful tool as you can test your model under a range of initial conditions, in a high throughput manner.
Copasi is also capable of performing parameter estimation, which allows you to input laboratory data into your model as parameter values and then fit your model parameter values to the data to “reduce the distance” between your model and your observations and reproduce in vivo representative behaviour. In addition, there are a number of optimization algorithms built into Copasi that can optimize your model towards an objective function, or find conditions under which the model behaves in some particular way. There are a wide range of algorithms pre-programmed into Copasi for these tasks including evolutionary programming, genetic algorithms, particle swarms, Praxis, Hooke and Jeeves and more. For the even braver modellers, Copasi can be used in conjunction with Gepasi, an older relative of Copasi that can be used to run multiple simulations simultaneously. For example, you can have multiple copies of a model representing a culture of interacting cells or systems and run multiple simulations on multiple interacting models!
Models can be imported and exported in xml and sbml format and ODE’s can be exported in LaTeX and MathML formats for transfer between different applications. Models from biomodels.net can be imported directly into Copasi and there is a feature to update model details from the Miriam database. There is also a command line version of Copasi that enables high throughput “automated” modelling processes to be run. The Copasi group is also working on a web interface enabling scientists to access the software through a web browser interface.
The comprehensive tool set available in Copasi provides a hugely powerful tool for the budding systems biologists to immerse themselves in the field of mathematical modelling and perform some fairly rigorous and comprehensive modelling techniques without prior experience of complex mathematical programming. It can also produce data for the biologist with a minimum of mathematical knowledge, providing some interesting incites for experimental hypothesis generation.
Copasi is available as open-source, and free for academic research from http://www.copasi.org, and is under continuous development by a core team of programmers as well as a community of users interacting through an active forum. The software is available for Windows, Mac, and Linux. If you’re currently wresting with Matlab or modelling in general, I would recommend Copasi as an excellent starting point to dive into the sometimes intractable world of mathematical modelling, particularly coming from a biological background.
Firefox maintenance – vacuum the sql database
August 24, 2009 by Steve · Leave a Comment
# Open the Error Console: Tools menu/Error Console
# In the Code text box paste this (it’s a single line):
Components.classes["@mozilla.org/browser/nav-history-service;1"]
.getService(Components.interfaces.nsPIPlacesDatabase).DBConnection
.executeSimpleSQL("VACUUM");
# Press Evaluate. All the UI will freeze for a few seconds while databases are VACUUMed
From lifehacker.com
can a scientist be “multidisciplinary”?
During this years inter-DTC systems biology students conference there was a debate session on the subject “can scientists be multidisciplinary?”. The purpose of the session was to debate whether students are better equiped for scientific research by specialising in a particular field or diversifying across fields. I have heard this debate a number of times since joining the Manchester DTC, which I believe stems from an inherent insecurity in the decision to train in the emergent field of systems biology. Many scientists have the desire to label themselves with an identity through their specialism and join other scientists sharing their label in an almost medieval guild like behaviour. These guilds then form alliances between other like minded individuals within and across Universities. This approach has worked well in the existing reductionist scientific world where research is focused on specific areas of interest, enabling funding bodies to quickly identify and recruit suitably skilled scientists to complete their projects. With the advancements in high throughput automation and computer science an increasing number of projects are pushing towards integrative research projects, combining data and experimentation from diverse scientific fields. These advances have culminated recently in the emergent field of systems biology that is driving a new holistic scientific approach through the integration of many scientific disciplines into multidisciplinary research projects. The existing system of training and recruiting specialist scientists has been adapted to encompass a higher level of organisation, utilizing multidisciplinary teams with a central management body coordinating the multidisciplinary communal effort. Problems arising from this new multidisciplinary group working has been in the area of communication with resistance from each of the parties to work with the other, or a resistance to consider the others ways of working, thought processes, or general scientific rationale. The project coordinators have tackled this by continuing the segregation and coordinating from outside each of the groups, minimizing or eliminating the requirement for the component researchers to interact. More recently however, systems biology has promoted a new, more radical approach of training the individual component researchers with the fundamental key skills of their project colleagues, culminating in the development of pioneering University doctoral training centres such as the MIB where classically trained specialists are re-trained in their opposite fields, combining wet and dry lab skills in a single researcher, and the first wave of “systems biologists” are beginning to emerge.
To return to the point of my post, there were representatives on the conference debate panel from Astra Zenica and Pfizer, and the inevitable question “what are you looking for when recruiting a systems biologist?” came up. I found the answer unsurprising, but disappointing. The large pharma companies are searching for mathematicians who can build them models of biological systems that they can use to direct their research. This statement wasn’t followed up by any of the academic researchers. I was left considering the future and relevance of “multidisciplinary scientists” in the wider world. Philosophically, I believe all scientists should be inherently multidisciplinary, enabling them to investigate the world around them and draw conclusion from whichever realm of science that is relevant to the question. I believe that every individual is capable to a reasonable extent to learn anything, and not just “their field” with the only barrier often being attitude and effort. However, in the real world you have to pay the rent and put food on the table, so the starving scientist must match their skill set with the market demand. Current scientific infrastructure in academia and the private sector is set up to employ the person who has the specific skills to complete whatever task is required that their existing assets in the organisation cannot. A multidisciplinary scientist therefore could be considered a “jack of all trades and master of none” and be continuously out-competed by specialists. Existing academic and industry development frameworks are still configured to develop individuals in a specialist role and multidisciplinary individuals don’t fit in their human resources skills matrix, making employment and development impossible to place within their company hierarchy. In addition, the current “group approach” of systems biology means that multidisciplinary thinking is often only required from those coordinating the project, and not the component individuals facilitating the work, and could be interpreted as an unnecessary diversion, deflecting from the development of a key specialism that would be of value to a potential employer. It gave me the feeling that the pharmaceutical industry is funding and promoting systems biology development with the aim of using it as a vector to cherry pick mathematicians that can be re-programmed with sufficient biological knowledge to adapt their mathematical skills to simulation of biological interactions, and the development of wet lab scientists an unfortunate by product. Mathematicians, after sufficient training in systems biology can manage the wet lab scientists and systems biology projects sufficiently to deliver the data required to populate the models and drive the biological hypothesis generation, with wet lab scientists a part of the process that is yet to be automated.
Just to qualify the above, I don’t intend for this post to sound of the “sucks to be you chained in the lab” general bench scientist rant. I believe that systems biology is a transitory scientific field born out of the lack of in situ data to build accurate real world simulations of biological systems. The wet scientists are employed purely to gather this data to populate the mathematicians models, which the mathematicians then use to generate hypothesis and direct the research. It is my belief that mathematicians are the multidisciplinary scientists in systems biology, and must be multidisciplinary for it to continue. The biologists on the other hand must continue to focus on specialisation to develop new measurement techniques, physically obtain the required information, and critically to retain their market value and employment. I believe that biological scientists in systems biology will eventually diversify into either their original fields, or new ones particularly synthetic biology, while systems biology retain the mathematicians and to a certain extent chemists who follow the computer science/simulation road. I believe that adopting a multidisciplinary approach for systems biology is essential for the mathematicians but this approach is detrimental, if not career suicide for biologists, who would be better directed towards classical fields, or for those seeking something new and akin to systems biology – synthetic biology.
I would like to gain comment on this post. I intended for it to be a bit reactionary and maybe inflammatory so I can perhaps incense some response and be proved wrong. I joined the systems biology road trip with the hope of gaining new skills that would drive a new career in biological sciences, and I am hoping for it not to have been a mistake! 
2009 Inter-DTC Systems Biology conference – Manchester MIB
June 27, 2009 by Steve · Leave a Comment
This year’s Inter-DTC systems biology students conference was held at our own Manchester Interdisciplinary Biocentre. Manchester was following on from Warwick’s excellent event last year on their home campus, and had invited a range of speakers from Manchester, Warwick, and Oxford’s systems biology doctoral training centers.
The talks were divided into sections covering many aspects of systems biology ranging across application to theory. There were a number of interesting keynote speakers. Dieter Weichart talked on “from ‘omics’ to systems biology, and David Broomhead gave an intriguing lecture on applying fractal maths to simulate the complex composition of the cell cytoplasm. Professor Broomhead has an excellent way of communicating complex theorem to the most mathematically inept (me!). Pedro Mendes presented a history of simulating biochemical reactions taking us back to the early days of punch cards and drive through size computers crunching away and amusingly producing the same graphs your quad core Intel 8gb DDR-3 powered nvidia SLi carbon footprint behemoth produces 
The students presented a diverse range of projects representative of the style of the doctoral training centre in each University. Oxford University gave an impressive visual presentation of their progress modelling blood vessels within the heart, building on the existing model of the heart by Noble. There were a number of talks ranging across modelling cell signalling, tracking cell movements, and bioengineering of microorganisms for potential biotechnology applications. In addition, there was also 2 interesting talks that diversified from the cell biology / microbiology themes, on modelling / “decoding” epilepsy EEG seizure data to provide new understanding of the underlying cause of the condition and provide potential technologies for predicting and managing seizures. One talk focused on absent seizures while the other focused on grand mal seizures, bother using different mathematical and statistical methods to search for patterns in the inherantly complex and chaotic brain activity.
The event was a great way to encourage students to communicate between systems biology DTC’s as well as building links for current and future research. I enjoyed the opportunity to meet with students working on areas similar to my own, as well as their supervisors who could give their own incite on the work that I was doing. This helps to broaden your understanding, as well as gain fresh ideas from people outside of your usual research group. After the conference we went for an excellent meal hosted by Professor Westerhoff and had a chance to interact in a more relaxed social environment.
Next year’s conference hopefully will be hosted by Oxford University, which would be a unique and priviledged opportunity to visit their prestigious campus, and experience their own blend of systems biology research.
tools of the trade
May 18, 2009 by Steve · 2 Comments
I’m a fan of open source software as an alternative to expensive commercial packages, and after being asked about various tools by colleagues and watching the lab splurge huge volumes of cash on expensive software I decided to compile a list of the stuff I have been using in my studies. Hopefully it might help others in the future from jury rigging powerpoint posters and watching 30,000 word documents go up in smoke at 3am when you inserted that last minute graph. There is also an excellent database of this kind of stuff over at open source alternatives.
If anybody has any other favourite gadgets or recommendations for the list let me know
- ApE
- ApE is an excellent tool for planning your cloning. Personally we use clone manager, but it’s expensive commercial software. ApE offers most of the features of clone manager and a few handy extra ones that the big companies don’t. You can draw plasmid maps, search for restriction sites, plan cloning (even simulate your digests with ladders), and even read ABI files to analyse your sequencing data. There are versions for Windows, Mac, and Linux. Recommended
- Bioedit
- Bioedit is a freeware nucleic acid sequence analysis tool with numerous alignment and online database functions. The essential tool for the molecular biologist
- Chromas Lite
- Free DNA sequence analysis tool. Limited functionality version of commercial package. Useful for quick anallysis of sequence house chromatograms.
- kbib / JabRef
- Open source bibliography software to keep track of article collections and simplify bibliography creation. JabRef is a Windows Java based reference library compatible with bibtek format bibliographies
- Mendeley
- Mendeley is an interesting reference manager allowing users to store bibliographies online and share them with other Mendeley users, forming project/research groups shared reference libraries.
- Texmaker / LaTeX
- Open source publishing software for Linux, essential for any student writing a thesis or other sizeable document. I highly recommend students attempt the steep LaTeX learning curve in favor of Microsoft Office. Save yourself last minute thesis and bibliography formatting hell and let LaTeX do it for you.
- TexnicCenter / MikTeX
- Windows equivalent LaTeX setup. TexnicCenter contains inline spell check and a nicer interface than Texmaker, but is Windows only.
- AbiWord
- If you just need a word processor avoid the bloat of open office and use AbiWord.
- Open Office
- The benchmark free office suite, rivaling Microsoft office and supporting open document format. I find problems in compatilibity with Powerpoint however, particularly since the release of Office 2007 but I haven’t fully tested the latest version 3.1 yet. However, barring compatibility with Office users you get a fully functional office suite for free. Also bundled as standard in Ubuntu Linux.
- Mozilla Firefox / Thunderbird / Sunbird
- Do yourself a favor and dump Microsoft Outlook for Thunderbird. Firefox is moderately web standards compliant and significantly more compliant than internet explorer. Sunbird is a fully fledged callendering application. The extensions available for each of the 3 packages extend their functionality and allow users to customize them for their own application.
- Foxit reader / Sumatra
- Adobe Acrobat reader has become increasingly bloated and resource demanding and currently weighs in at a 41mb download. Free alternatives Foxit, pdf-xchange viewer, and the ultra light weight Sumatra are excellent alternatives to Adobe.
- PDF Creator / doPDF
- Windows users can create PDF files using either of these free tools. The software installs a virtual printer that will create a PDF document from anything you send to it. An excellent alternative to Adobe Acrobat suite.
- 7zip
- Free archiving tool compatible with all major file formats (zip, rar, tar etc).
- PSPad / Notepad++
- Free text editor compatible with many programming languages. Tabbed interface, inline programming syntax and spell checking, and loads more. Notepad++ also does the same but is more lighweight.
- Dia
- Free diagram drawing tool. Ditch microsoft office / powerpoint clipart. Outputs in various image formats and post script to drop straight into LaTeX or Office documents.
- Inkscape
- Open source vector drawing package supporting scalable vector graphics (SVG). Free software now rivals adobe Adobe Illustrator
- Scribus
- Open source desktop publishing package. Open source desktop publishing package orginially developed for designing scientific posters now rivals the likes of Adobe InDesign.
- Paint.net / the Gimp
- 2 free graphics packages that I find indespensible. Paint.net is great for making quick image edits but requires the dot net framework. the Gimp is a comprehensive graphics package rivaling Adobe Photoshop with compatibility with photoshop filters. Available for both Windows and Linux, the interface takes some getting used to but the software can do pretty much everything found in the more expensive proprietary graphics packages.
- ImageJ / Fiji
- ImageJ is the current software of choice for image analysis with a wide range of extensions and macros available. Fiji is the Linux port of ImageJ.
- IrfanView
- Freeware image viewer compatible with nearly all image formats
- Google Picasa
- Free image viewer with basic editor functions and facility to upload and share images through web albums.
- Kompozer
- Updated version of nvu WYSIWYG web design package. Save yourself the cost of Dreamweaver.
- Antivir / Avast! / AVG
- Free antivirus for Windows. Antivir is less resource intensive than Avast! and AVG. Keep an eye on VB100 to see which retain their virus detection certificate.
- Malwarebytes antispyware / Spybot S&D / Adaware
- Spybot S&D was the standard in spyware removal but recently lost out to Malwarebytes, however browser immunization and tea timer still provide superior protection to the competitors. Adaware is resource intensive and not as stringent as Malwarebytes or Spybot.
- CCleaner
- Clean the sh1te from your Windows installation and free up disk space.
- Defragler
- Freeware disk defragmentation tool. Run this once a week or month to keep Windows responsive.
- Pidgin
- Got msn? Got ICQ, yahoo, AIM, AOL, Jabber, myspace, IRC, and a myriad of other online communication tools as well? Connect to them all simultaneously without being bombarded with adverts from the proprietary IM clients.
- Windows 7
- Depressingly awesome next generation operating system from Microsoft. Join the beta program and trial the release candidate for free.
- Ubuntu
- Ready to roll open source / freeware Linux operating system complete with office and graphics applications. Synaptic package manager provides thousands of additional software packages. Ubuntu provides a friendly introduction to using Linux that can help migrate from Windows before diving into the more demanding distributions.
- Linux Mint
- Based on Ubuntu, Linux mint includes proprietary 3rd party drivers and multimedia codecs that Ubuntu doesn’t package, and includes some fixes like the wireless problems that continue to plague Ubuntu.
- Portable Apps
- If you want to go all the way and not even have your own operating system Portableapps.com has created a number of applications modified to run from a USB memory stick so you can take your favorite desktop applications wherever you go. You also don’t have the security hastle of working on a public computer as all your data and temporary files never leave your pen drive.
Jaunty Jackalope
March 27, 2009 by Steve · Leave a Comment
Ubuntu 9.04 – Jaunty Jackalope beta has hit the Canonicle servers. Full release is due at the end of April. I’m going to give the 32bit desktop edition a run out on my laptop over the weekend.
9.04 promises Open Office 3.01 and the new ext4 filesystem which is reporting faster boot up times. No 2.6.29 kernel however as the development team will freeze the feature set before its release. 9.04 will ship with 2.6.28 stable. Ubuntu 9.10 will be shipping with 2.6.30 or 2.6.31… or neither if we’re all credit crunched to oblivion :p
FEBS feedback
March 18, 2009 by Steve · Leave a Comment
There wasn’t much opportunity to obtain internet access at this years FEBS 2009 conference. We had a busy schedule of lectures from 8.30am to 10ish, followed by practical workshops, blackboard sessions, and discusson groups until lunch time. We were given a break from 1-4pm to take in the local scenery, particularly the ski slopes after which we returned for lectures and discussion sessions until 6pm. The evenings involved a meal until 7pm after which we returned for poster sessions and group discussions until 11pm. This was a challenging schedule and crammed an enormous amount of science into each day.
I particularly enjoyed the talks from Roger Brent from Berkeley, CA and Ron Weiss of Princeton as these were particularly relevant to my work in synthetic biology. The electrical engineering approach of Ron Weiss was very useful in conceptualising the design of synthetic gene circuitry and his work in mamalian cells was inspiring. Roger Brent provided some practical methods of measuring outputs of gene circuits and some useful open source software tools and lab methods that will greatly benefit my project.
There was also some very good talks from Eda Klipp on the mathematical modelling of biological pathways, and combined with practical copasi sessions with Frank Bruggerman modelling MAPK signaling pathways. There was a lot of practical worked examples combining wet lab experimentation with mathematical modelling that gave a real incite into the development of systems biology and the application of it’s approach.
Denis Noble popped in for a keynote lecture on his development of the heart model and provided a unique opportunity to gain an understanding of the processes he went through in building one of the pioneering projects in systems biology. There was also a nice opportunity to meet with him and we received a signed copy of his book - the music of life. It is always an inspiration to hear Denis Noble speak and I would recommend any scientist to take a look at his talks on youtube.
I will update more info as I get time, as it’s full steam ahead on my return to Manchester.
FEBS systems biology advanced lecture course 2009
March 4, 2009 by Steve · Leave a Comment
This year our DTC studentship will be attending the FEBS systems biology advanced lecture course in Alpbach, Austria.
I have booked in for the “physiological systems biology” and “modeling cell biology workshops”. Hopefully both courses will provide valuable training for the dry component of my project.
I will be updating from Austria if I can get internet access.