Six suggestions for spring cleaning your (scientific) digital life

Laura is back with a slightly different post for today, however something that I think could be very helpful for researchers of any discipline and any stage! We hope some of these will be of use, let us know if there are any we can add to the list – would be excellent to get a running list!

 

1) SciCurve: For entering a new field of research

Immersing yourself in the literature of a new field can be daunting. For me this is typically the part where I’m most prone to chronic procrastination – I endlessly skim articles and save hundreds of papers that never get read.
SciCurve maps out the ‘literature landscape’ relating to particular keyword/s in an interactive way which is way more helpful than the linear lists of publications found on PubMed or Google Scholar. View the search results as trends, networks and maps. Find out who the big dogs are (most highly cited authors).
Apparently there is option to integrate with reference managing software such as Mendeley or Zotero, but I’ve been unable to get this to work. If anyone manages it let me know how!

Hover over each node to see the relevant citation.

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2) The PaperLink

This useful browser extension enables “1-click” pdf downloads from PubMed via the blue boxes that appear on PubMed search results. It’s not available for all publications, but anyone familiar with clicking through PubMed links to journal links to pdf links will appreciate the time saving where it does work.
Available for Chrome, Safari and Firefox.

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3) Mendeley / Colwiz: For Managing References

If your life even slightly involves downloading publication pdfs: you should be using one of these by now. There are plenty of options – Mendeley, colwiz, readcube, zotero…but they all mostly do the same things: storing, organising, viewing, highlighting, annotating pdfs. Free cloud storage enables access to documents across devices.

My favourite Mendeley tip is to set up to ‘watch’ a folder (e.g. the ‘Downloads’ folder – or even better – a Dropbox folder), from which it will automatically import files as you download them. There is no need to move downloaded pdfs, or change the useless file names like ‘Natureyr2382dhksfkmm.pdf’, as Mendeley can also be set to organise pdf’s into folders (by Author or Year etc.), and rewrite file names as you choose. My PDFs are enviously well organised thanks to these features.

[Ed – I also completely recommend mendeley for referencing – it changed my (writing) life and is SO much better and user intuitive than EndNote, with the free plug in for word. Since Laura recommended it whilst on placement together a couple of years ago I have told anyone (literally) I know are writing up, and always get the same response! Another useful feature is shared folders, so say a lab group can add interesting papers and share within – Livvi]

4) SNAPGene: For Molecular biology

Someone recommended SNAPgene to me last week, and my understanding of molecular biology basically tripled. Use it to view annotated vector maps (downloadable from addgene: http://www.addgene.org/vector-database/ ), identify restriction sites and design primers. There is probably much more. I’ve tried a few different molecular biology/sequence programmes but this one feels easy to navigate and nice to look at. The free version does have a few annoying restrictions (like not being able to edit sequences) but nothing major (just paste in a new sequence).

5) Generic lab calculators: For Buffers & Dilutions
I think this is something everyone struggles with and personally causes me a lot of stress and confusion!

Buffers: http://www.bioinformatics.org/jambw/5/4/index.html
Dilutions: http://www.sigmaaldrich.com/chemistry/stockroom-reagents/learning-center/technical-library/solution-dilution-calculator.html

6) Raw: For visualising data beautifully

For websites and posters/presentations/elaborate lab books.
Honestly – my data would never fit this format, but I’m including it here because it looks so nice.

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Let us know if you’ve used any of these before, or for anymore suggestions we can add to this list!

Written by Livvi Harris

Livvi Harris

I am a first year PhD Wellcome Trust PhD student at the Cambridge Stem Cell Institute currently carrying out a year of rotations, so I can’t quite tell you what my PhD is in yet! I am an ex-pharmacologist (or maybe current?!) from the University of Bath, with 15 months experience of industry after working for the oncology pharmacology team at MedImmune in Cambridge for my placement year.

2 thoughts on “Six suggestions for spring cleaning your (scientific) digital life

  1. Hi Vladimir, thanks for your comment. I just had another play with SciCurve and managed to save references straight to my Mendeley account – this is a nice feature!

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