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
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.
blog rebooted
March 3, 2009 by Steve · Leave a Comment
I have reactived my blog to keep an account of my work in systems biology, inspired by Professor Douglas Kell’s blog at the BBSRC. I am also due to attend the FEBS systems biology conference in Austria next week and would like to record the event.
I will see where it goes…
LaTeX
June 11, 2008 by Steve · Leave a Comment
I have been thinking for a while about the best tools to use when writing scientific reports throughout my PhD. Systems Biology combines mathematical modelling with wet lab experimentation. For me, writing equations alongside experimental data is a new experience and I was unsure how to insert this kind of information into an electronic document. There is always Microsoft equation editor, but this didn’t seem to produce the same quality of script as seen in scientific publications. I have recently favored the open source applicaton MathCast for creating equations as it outputs both as images and mathml which makes it quite versatile. I had been aware of LaTex for a few years but had many problems compiling something usable in Windows and had been too lazy to bother learning the LaTex coding to perform tasks that Office could do with a mouse click. I found it difficult to break into the LaTex scene and had rebounded back to Office and my toolbox of open source applications. Recently I have migrated over to Ubuntu and ventured into LaTex again using the synaptic package manager to compile the myriad dependencies for LaTex. This went ok and I got myself a working LaTex environment, however I still couldn’t be bothered to “code” my documents when I could just churn out an office document.
Today I stumbled on Lyx, a WYSIWYM LaTex editor. WYSIWYM is “what you see if what you mean” and utilizes a word processor style interface to plug into MikTex. For new people, idiots, and combinations of the 2 like myself, this enables the user to construct a LaTex document using a minimal understanding of the markup language but without losing any of the capabilities of LaTex.
A comprehensive review can be found here. I have to get my head around structuring a LaTex document, however Lyx provides the “leg up” to begin escaping the comfort blanket of Microsoft Office.
Ubuntu 8.04
May 11, 2008 by Steve · Leave a Comment
No updates in a while due to work commitments. Just a quick post before bed to comment on the latest release of Ubuntu Linux. I have been tinkering with Ubuntu for a couple of years after brief forays into Mandrake, Peanut, and SUSE. I have had a few problems with driver and general compatibility issues between Linux and the rest of the world using MS Windows and stuck to XP. I tried out Ubuntu as it was the first distribution that moved away from supplying the user with 6 CDs containing a myriad of applications all doing the same thing, installing from a single 700mb CD with everything you needed. My course here at Manchester provided an Acer Travelmate 4230 laptop which we have been using for general report writing and more recently mathematical modelling with Mathematica and Copasi. I had a play with various versions of Ubuntu 6 and 7 but could never get it to recognise all the integrated hardware and ended up back with XP again.
Earlier this month I downloaded the latest Ubuntu 8.04 and gave their new Wubuntu windows installer a go as I could have a quick play and delete it without having to re-partition my hard disk. Ubuntu installed alongside XP with a smooth bootloader and ISO image instead of dual boot. I was stunned to find the operating system happily detecting all the integrated intel hardware on the laptop, the widescreen resolution, and even the integrated 3D graphics accelerator to provide the full bells and whistles Compiz Fusion desktop. A week later and I haven’t booted back into XP! The OS migrated all my user accounts automatically from XP and mapped the old partition as a drive within Ubuntu. I downloaded a couple of extra packages like Amorak and Thunderbird and I’m seriously considering waving goodbye to Microsoft for my future work. The speed gained from the Linux filesystem is considerable and the integrated synaptics package manager makes downloading additional software and updates simple.
I feel version 8.04 is a significant step forward for the Ubuntu community and a serious contended as a mainstream desktop operating system. I would seriously recommend anybody who is considering an expensive upgrade to Vista or Apple give it a try before shelling out.
The revolution is here 