Jack Simpson
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Jack Simpson

Strategy consultant and data scientist

    ResearchThoughts

    Essential Free Tools for Research

    by Jack Simpson April 13, 2014
    written by Jack Simpson

    I commenced my PhD in bioinformatics at the Australian National University about a month ago and thought I’d share some of the tools I’ve found absolutely essential. All of these tools are free to use (some do have paid plans, however at this point I haven’t had the need to sign up for them).

    1. Evernote + Evernote Web Clipper: Once I started to really get into using this tool, I couldn’t understand how I’d lived without it before. Now I can clip snippets from web pages for later reference, write notes from a seminar I attended or upload a Python script and have this all in one easily searchable (and tag-able) location. There’s also a plethora of phone/tablet apps which work really well.
    2. Wunderlist: While I tried to use Evernote for keeping to-do lists, I found that this simple yet powerful program (with support for PC, Mac, phones and tablets) worked extremely well for keeping track of my tasks.
    3. Dropbox: I do all my work within the Dropbox folder on my computer. This way, when I move between computers everything is synced and backed-up. While I have tried Google Drive before, the lack of support for Linux as well as issues with syncing have led me back to using Dropbox.
    4. Zotero: Zotero is a referencing manager with a browser plug-in which is fantastic at importing the bibliographic details and pdf of the paper from the web. It can also sync between computers (although you only get 300 mb of free sync space). While I have used the alternative referencing manager Mendeley before (which has 2gb free sync space and a brilliant program which enables you to annotate your pdfs), the Mendeley web import tool was so bad at importing the bibliographic details and pdfs of papers that I went over to Zotero.
    5. VirtualBox: If you find yourself having to use a lot of Linux-only tools (or you like the fact that you can install entire programs with multiple dependencies merely with the command ‘sudo apt-get’) but don’t really want to set up anything permanent , then VirtualBox could be the way to go. Its a free program that allows you to run a whole operating system on your computer within a window just like any other program.
    6. Coursera/EdX/Udacity: These websites offer free courses from great unis in everything from computer science to genomics.
    7. Stack Overflow/Biostars: Great websites for asking questions relating to programming or bioinformatics. If you can’t find anything after searching Google, then this is the place to post your question.
    8. Twitter: Although this can be a bit of a time-waster, I find that by following other researchers in my field and research organisations I can hear about new papers or tutorials.
    9. Google Plus: G+ may not be as popular as Facebook, but I find most of my programming friends tend to be quite active on it and if you join one of the programming communities it can be a great place to learn new things or ask questions.
    10. Google Scholar Alerts: Sign up to receive emails whenever the keywords you select are published in a paper.
    April 13, 2014 0 comment
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  • ProgrammingThoughts

    Explicit is better than implicit

    by Jack Simpson March 7, 2014
    by Jack Simpson March 7, 2014

    Line two of the zen of Python reads “explicit is better than implicit” and until relatively recently I never truly appreciated the wisdom of those words. My change of heart stems from…

  • ProgrammingTutorial

    R Tutorial

    by Jack Simpson May 9, 2013
    by Jack Simpson May 9, 2013

    This tutorial is a beginners guide for getting started with R, once you complete it you should have R installed on your computer and be able to import data, perform…

  • ProgrammingResearchTutorial

    BioPython Tutorial

    by Jack Simpson May 6, 2013
    by Jack Simpson May 6, 2013

    This tutorial is a brief overview of what you can achieve using the Python BioPython module. Although I’m hoping to write up some more articles on this site for beginners…

  • ProgrammingResearchTutorial

    Pyral Project

    by Jack Simpson May 6, 2013
    by Jack Simpson May 6, 2013

    Pyral (Python + Viral) was the name of a project I worked on in Dr Joanne Macdonald’s lab between September 2012 – January 2013 (although I am still providing tech support…

  • ProgrammingTutorial

    Python sys Module

    by Jack Simpson February 8, 2013
    by Jack Simpson February 8, 2013

    The main use I’ve found for the Python sys module is allowing command-line arguments to be made to a script. Here is an example of how it looks: This script…

  • ProgrammingTutorial

    Python os Module

    by Jack Simpson February 6, 2013
    by Jack Simpson February 6, 2013

    You can use the Python os module to send commands out to the operating system. Through os you can do anything from changing the current working directory through to listing…

  • LinuxTutorial

    Useful Linux Commands

    by Jack Simpson February 6, 2013
    by Jack Simpson February 6, 2013

    Linux is an operating system – similar to Windows or Mac. It is freely available and very popular amongst researchers and programmers. Since many of the scripts you write will…

  • ProgrammingTips/Bugs

    Parsing CSV Files in Python

    by Jack Simpson February 6, 2013
    by Jack Simpson February 6, 2013

    Almost anyone doing research at some point will have to input or extract data from an Excel spreadsheet. However, it is possible to export an Excel file as a .csv…

  • Programming

    Logging into PuTTY with Perl

    by Jack Simpson February 5, 2013
    by Jack Simpson February 5, 2013

    When you use the SSH client PuTTY a lot, it can become quite tedious selecting your server and then writing in your username and password. That’s why I decided to…

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