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
choose your weapon
March 4, 2009 by Steve · Leave a Comment
Faced with the task of creating a PhD dissertation over the next 3 years I briefly investigated alternatives to the standard Microsoft Office suite. I had played with Lyx last year but I quickly found myself outgrowing the WYSIWYG interface as I learned to code. I also required a reference manager as my literature review was comprising over 200 references and the easiest way to get these software packages to interact was to dump the crutches.
I have tried to stay away from Microsoft Office this time as I have spent many years wrestling with auto correct, auto formatting, and frustrating middle of the night sessions watching figures jump around pages and printed documents looking nothing like what is on the screen, not to mention the random events that will occur when I send it to another machine. I have also moved over to Ubuntu 8.10 as my primary operating system and adopted open office. Still, the prospect of writing a thousand page document in MS or open office didn’t feel practical. I stuck with open office initially and needed to investigate a reference manager that would play with it. The Universities recommendation was Endnote but this was out on my Linux box so I began with bibus as it can store your references in an sql database and I had visions of being able to keep my library on a web server. Unfortunately I ran into problems when exporting the database – it wouldn’t, and it didn’t play very nicely with open office, requiring time to install pipelines to pass data between the two applications, and generally being unpleasant if I wanted to rapidly throw in reference on the fly. Bibus also had problems finding references in pubmed and often couldn’t find them even with PUID numbers. As with bibus, Endnote also appeared to require a break in the writing flow to input a reference.
I cut my losses with office suites and took the plunge into LaTeX proper with Tex Maker and kbib. Kbib so far hasn’t failed to find a reference search I’ve thrown at it, and imports citations from the web and exports my library into various RIS, xml, and endnote formats ensuring some future compatibility/portability. Tex Maker isn’t the best LaTeX editor and is still digital blasphemy for hardcore vim or Emacs users, but I like the help it gives me with the code and syntax. Kile is better with in-line spell check, but texmaker gives me a native gnome application and I can do bulk spell checks periodically. The code was a hurdle at first, but after a few pages I had grasped a set of basic formatting codes and LaTeX was allowing me to just write and not think about headings and margins, and where the heck figure 9 just went. I also seemed to grasp the equation editor relatively quickly and found it fairly straight forward to use. It isn’t as simple as the MS and open office equation editors, but allowed me much greater control. The real power of LaTex for me has been the labelling and tagging capability. I can just tell LaTex what’s a figure, equation, diagram, etc and carry on writing. References are much the same, just inputting the library identifier and carry on with the text. The compiler will then number and reference them automatically, which is an enormous time saver and doesn’t break the flow of writing. Inserting a new figure in the middle of a 300 page document at 3am the night before submission is a horror I have experienced plenty of times before in Office, and manually curating a bibliography is impossible this time. LaTeX isn’t all loved up for the user though. Document compiling can be a daunting experience when a random $ sign can give you a completely incomprehensible error message at 2am requiring an hour of debugging. This is where MS Office scores a few dozen points back. LaTex GUI’s could definitely improve the bug hunting for “noobies”. After 3 months though I am fairly happy now creating all of my documents in LaTeX and would recommend anybody creating anything greater than an essay to use it, as you can quite literally just write and let the compiler worry about everything else. Happy days.
For our impending conference visit I attempted to create a scientific poster in LaTex. Error. I gave this a good go… honest. However I found my LaTex Jedi skills to be somewhat under developed and there just wasn’t enough control over the layout without a serious time investment in learning some more advanced code to complete the task. The University recommended MS PowerPoint, however an A0 document with images in Powerpoint is a nightmare without a quad core processor and as much ram as you can stuff inside the case. Open Office also requires an enormous amount of time to load and save this kind of document, especially converting between MS office formats. This time I turned to Scribus, an open source desktop publishing package that was designed by a LaTeX user also struggling to create scientific posters and struggling with the lack of available software. I hadn’t really used Scribus before but found it very easy to input text boxes and images, with fine control of positioning using a WYSIWYG interface. Scribus also exports as PDF so you can export your documents and send them to the printers moderately confident of what will come back. Scribus is also infinitely more sophisticated than powerpoint with support for scalable vector graphics and templates for almost any kind of document. Happy days again.
My next challenges are finding some alternative graphing software to escape Excel and some training in Matlab.
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.