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.
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.
Ubuntu keyboard shortcuts
May 13, 2010 by Steve · Leave a Comment
Workspaces
* Ctrl + Alt + Left/Right/Up/Down arrow – move to the workspace in the given direction
* Ctrl + Alt + Shift + Left/Right arrow – move the current window to the workspace in the given direction
* Super + E – “expo” effect, shows all workspaces (move windows with left mouse button, zoom to a workspace with right mouse button)
Window Management
* Super + W – “scale” effect, shows all windows in current workspace (left click selects window, middle click closes window, right click zooms window)
* Super + A – “scale” effect, shows all windows
* Alt + F10 – toggle maximize current window
* Alt + F9 – minimize current window
* Ctrl + Alt + D – toggle show desktop
* Alt + Middle mouse button – resize window
* Alt + Left mouse button – move window
* Alt + Right mouse button – window menu
* Alt + F7 – move current window (without holding down mouse button)
* Alt + F8 – resize current window (without holding down mouse button)
* Alt + Tab – switch windows on current workspace
* Ctrl + Alt + Tab – switch windows on all workspaces
Accessibility
* Super + Mouse wheel scroll – zoom screen
* Super + Middle mouse button – draw rectangle to zoom to
* Super + N – invert colours of current window
* Super + M – invert colours of screen (Compiz is configured for this shortcut, but the messaging indicator seems to have taken it over so it doesn’t work)
Open Office tweaks
May 8, 2010 by Steve · Leave a Comment
In tools -> Options -> Memory:
Reduce the number of Undo steps to a figure lower than 100. Websites suggest 20 or 30 steps.
Under Graphics cache, set Use for OpenOffice.org to 128 MB (up from the original 6MB).
Set Memory per object to 20MB (up from the default .5MB).
Set the number of objects under Cache for inserted objects at 20.
Check OpenOffice.org Quickstarter.
Now highlight Java on the left panel, uncheck Use a Java runtime environment
Exit and re-load open office.
mathematized
November 17, 2009 by Steve · 4 Comments
Started a pet project trying to code up the equations from the Mackay and Glass, Oscillation and Chaos in Physiological Control Systems (1977) paper. I need to learn some maths, and some maths programming to broaden my skills beyond wet lab molecular biology. Copasi is ok but it’s reaction based and I worry a point and click interface wont get me a job when I graduate. However, I am rapidly lost in Matlab and Mathematica. I chose Matlab for compatibility and support in the MIB community, but drifted into Mathematica as it seems easier to program using symbolic maths. Both are ok with algebra, then I just get blown away doing anything dynamic like ODE’s. If anybody reads this and has any good tutorials for programming up ODE systems in either/any computing language please let me know :/
Ubuntu 9.10 countdown
October 27, 2009 by Steve · Leave a Comment
Karmic Koala is out, and it’s biting at the heals of Windows 7 and Snow Leopard.
“You are capable of choosing your own destiny. The question is, which path will you choose?”
I’ve been running Windows 7 on a dual boot with Linux Mint for the duration of the Windows 7 beta program. Windows 7 has proved to be a worthy successor to Windows XP, and dragged Microsoft from the pit of despair they hurled themselves into with Windows Vista. In the wake of Vista and the iPOD, the Mac community was able to plough forward with OSX, gaining increasing ground with the macbook pro and air, and more recently had an update from Snow Leopard providing increased speed and some tweaks to their interface. Ubuntu peaked with Jaunty Jackalope and finally released a Linux distribution that gave the Linux community a foothold in the home desktop market. Hardcore Linux users balk at Ubuntu and the heresy of proposing a pre-built linux OS. It has been the long tradition that Unix users compile their own OS and applications, custom built for their own machine, learning the code along the way. There is a steep learning curve for many computer enthusiasts who seek the stability and speed of a Unix OS, but lack a lifetime of dedicated study in the dark art of the command line. Ubuntu broke the mold and provided a generic ready to roll Linux OS that was completely free of any proprietary drivers and codecs, so it could be distributed in any country to any hardware and enable everybody to use a computer regardless of wealth.
Ubuntu 9.10 (Karmic Koala) was released yesterday and continues to build on the improvement of intrepid ibex and jaunty jackalope. I’ve installed a copy of the 32bit desktop edition on a Dell XPS M1530. Installation was much the same as previous version 9 incarnations, with some graphic improvements. Drive partitioning was straight forward enough and it will sit alongside the existing Windows 7 partition without a problem. The OS installed in about 15 minutes and grub picked up the Windows installation to dual boot. I don’t like the new login window. The old version was more streamlined, with the current version requiring me to click on my account and enter my password, even though I’m the only user account on the machine. They also seem to be increasing the number of animated splash screens during the login, where 1 is unnecessary in my opinion. Get to the desktop and stop wasting computer cycles on spinning logos and flashing lines.
Ubuntu comes with no proprietary drivers so I had to install the latest nvidia driver set and download broadcom wireless drivers. This would be a major problem if I didn’t have ethernet internet access as straight away my laptop can’t connect to the internet. Fortunately I do have a wired connection so I could just grab them from the snaptic repository. This wouldn’t be obvious to the casual computer user though and would most likely, from their perspective, brick the machine and send them back to Windows / OSX. After this brief inconvenience I added in the restricted repositories and downloaded all the 3rd party codecs for multimedia playback and I have a ready to go OS again. DVD and MP3 playback is excellent in Totem player and rhythm box. I downloaded Exaile and VLC for myself but the pre-installed media playback tools are excellent. Ubuntu 9.10 comes with Firefox 3.5 which is much faster than 3.x previous versions, with improved Java engine. There is no pre-installed Thunderbird or Sunbird which I don’t understand (considering Firefox is there), instead choosing Evolution, which I haven’t used so can’t comment on. Ubuntu comes pre-loaded with Office 3.1.1 which is more than sufficient for word processing, spreadsheet, and presentations, supporting open document format and mostly compatible with Office 2003 (some compatibility with Office 2007, but personal experience has been bad with powerpoint 2007). Pidin IM has been replaced with empathy in this karmic. Empathy is compatible with all the major IM clients, as well as pidgin’s facebook chat plugin. 9.10 uses the ext4 filesystem as default providing faster data access speeds than previous ext3 and Windows ntfs. Copying files between ntfs and ext4 is noticeably quicker, and it boosts the OS bootup time considerably. 9.10 has also implemented a new “software centre” in place of the add/remove programs in 9.01. This is a streamlined equivalent of the old application, grouping software into easy to navigate sections for first time users. Personally I use the synaptic package library but it’s very useful for new users to find their way around the huge library of additional software that is available.
One of the newer implementations has been Ubuntu one – an online storage drive from canonical providing 2gb of free storage. I found this service to be less reliable than dropbox, which can be installed as a 3rd party application. It had some problems syncing my latex documents in my home folder when I made frequent changes. It was a beta application in Ubuntu 9.04 though and I might give it another go in 9.10. It’s still not bad to have 2gb free synchronized file storage out of the box for free, and an interesting feature that isn’t included in Microsoft or Apple’s OS.
For the complete list of the updates in Ubuntu 9.10, check out the new features page at Ubuntu.com here.
So for the grand price of £0 you get a ready to rock operating system in 32 and 64bit flavors that can (after a little bit of downloading) play high definition movies, music, do all your graphics and office work, surf the net, and send your e-mail. I hope Ubuntu continues to develop in the future, and spin off distributions like Linux Mint build on the Ubuntu base providing custom variations for any perceivable application. Hardcore Linux users might balk at the ethics of Ubuntu but it provides a shallower learning curve for new users like myself to experience the Linux world and break the monopoly of Microsoft and Apple in the home computing market. Once familiar with the environment it enables more serious users to move into the realm of Arch and even Gentoo, eventually compiling their own OS and joining the ranks of the command line battle hardened linux community.
Socialist computing has arrived.
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.
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.