Toolkit for Biologists: top 10 items to keep in your “work-pocket”
Written by Isabelle
In academia, you will find yourself writing various forms of texts often : your thesis, your papers, reviews, grant proposals, protocols, etc. For all of this, you need to read, create, format, edit, analyze and represent your data in visual and text form. Here’s a useful list of tools to make this process more manageable.
Microsoft (MS) Word is the most commonly used text editor. Because of how widespread its use is, it’s easy to get help if you’re struggling with it. Every beginner has been perplexed by the annoying phenomenon of the text moving around when you add a picture or a table, but overall, it promises ease of use. LibreOffice Writer is a free, open source software quite similar to MS Word. LyX is a more complex tool based on LaTeX typesetting. It’s an open source software mainly used by scholars, which requires you to learn the markup tagging convention to format the text. This takes some time to learn, but the rendering is high quality (especially for mathematical formulae).
After collecting, analyzing and compiling your experimental data, you will have to visually represent them. You will also need to plot quality graphs for your publications or congress presentations. Again, the most common tool is from Microsoft, MS Excel, which is user friendly and very handy to make a quick graph. However, the quality of plots is not up to the standards of high-impact journals and does not allow one to plot e.g., a scatter plot. GraphPad by Prism is a statistical software broadly used to plot graphs. You can perform your statistical analyses and directly plot the graph with good quality. Unfortunately, it is not free. Similarly to GraphPad, SigmaPlot and Origin are not free and allow both analyses and graph plotting. However, their functionalities are broader. We can also recommend MATLAB for those who are already familiar with this software.
Vector Graphics Software
To make professional figures to represent your data, it’s essential to use a vector graphics software. Many people are still using MS PowerPoint, which is a good solution if you are a novice but does not allow you to reach that professional, top-publication level look. Vector graphics allow you to design and manipulate your pictures, tables, and all the graphic elements contained in them in such a way that they can be scaled and still maintain the same resolution. Moreover, you can embed different types of data from different sources with different extensions. The most common commercial software are Adobe Illustrator and Adobe Photoshop, which have similar functionalities and can also be used together, to link a Photoshop file to the figure you are making in Illustrator. Most institutes provide Adobe licences to their employees. Corel Draw is another commercial software that is offered by many institutions. As for the two Adobe products, plenty of online tutorials are available. There are some free alternatives too, such as Inkscape. To create nice illustrations, you can also use the website Bio Render with premade scientific icons and templates.
Analysing the statistical power of your data is essential. While most statistical software are also a tool to visualize your data, some softwares have a more professional graph plotting visualisation and others have better algorithms for statistical analysis. You could however use two different softwares, one for your main statistical analyses and another to plot your graphs. If you are not a pro in statistics, GraphPad and SPSS are a good choice for you. They are both commercial softwares available at many institutions. If you have good typing or programming skills, you can use R or MATLAB.
Reference management is essential to keep track of references, create your library and order references per category. You will also need to incorporate your citations in your text document. Check out our previous post to know the pros and cons of various citation tools.
Scientific Paper Monitoring
To keep your bibliography up to date, you have to monitor the publication of papers in your field. You can of course visit the websites of your favorite journals regularly but it’s laborious and time consuming. One solution is to use aggregators of RSS flux gathering news feeds from different online sources. If you want to know more about it, check our previous post on Feedly. You can also set up automatic NCBI alerts with specific keywords, to receive emails each time a paper containing your keywords is published.
What’s the best way to digitally create to-do lists, organize your ideas, notes from seminars or lab meetings, experimental protocols, etc.? Digital files are very practical because they can be accessed from everywhere, easily shared with your colleagues and collaborators, and are all in one place (rather than a bazillion of notebooks). The most common tools are MS OneNote, Google Keep, Apple Note or Evernote. They allow users to drop images, create lists and attach files. If you need a collaborative workspace, MS OneNote, Google Drive, SciNote or other project management tools are a good option.
Computers and hard drives can get corrupted. When this happens, it’s a catastrophe. The loss of months or years of work. You have probably already saved (if not: do it!) your data on the server of your lab, but you never know what can happen to this one too. It is therefore also important to save your dataonline. There are several options, from Dropbox to Google Drive to the cloud. Make sure you always have enough GB to save all your data.
Image Analysis Software
As a scientist, you often collect pictures taken from microscopes or cameras. To capture beautiful images of your experiment, we advise the use of FIJI (Fiji Is Just ImageJ), an open-source software similar to ImageJ (NIH) with more plug-ins already installed. It provides many tools to analyze pictures and improve the rendering. Amongst its many applications are: merging pictures, adding scale bars, increasing the contrast, analysing the number of cells, and measuring areas. To work on your pictures, you can also use the microscope’s analysis software – for example, Zen for Zeiss or LASX for Leica. Each of these software has a free basic version allowing you to perform the initial image analyses. Alternatively, you can use MATLAB.
English Language Skills
If English is not your mother tongue, writing in this language can be difficult, depending on your origin. To improve your communication, you can use Grammarly for English language editing. It can be downloaded for free online, and helps you eliminate typos by pointing out grammatical and spelling errors. A nice tool to avoid the overuse of words is Thesaurus, a website which gives you synonyms and antonyms. It’s a good way to improve your vocabulary and enrich your text. You can als use Lexico.com, an online website from Oxford’s Dictionary that serves as an online vocabulary.
We hope you can communicate your science even better, armed with these nifty tools! :)
Written by Isabelle Arnoux; Edited by Radhika Menon. Featured Image: NGC/Design.