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.
About Steve
http://www.biology.utah.edu/jorgensen/wayned/ape/
has the ability to color based on a feature list, etc etc.
good tutorial here
http://openwetware.org/wiki/Arking:JCATutorialIntro9
Hi,
thanks for reading my blog
I will add ApE to the list. I had used it last year. There is a really useful feature to search for restriction sites that aren’t present, which I used for inserting custom sites by directed mutagenesis. Our lab has a copy of clone manager which I’ve found to be indispensable and although I don’t normally use commercial software, it’s well worth the money. A colleague of mine swears by serial cloner as well, but I haven’t used it.