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Freeware for scientists

Posted by on February 6th, 2012

After commenting on a previous post, I’ve decided to make my own post about freeware I use regularly that other scientists might find useful. All of these are available for Windows, Mac and Linux as far as I’m aware and come with various price plans if you want more storage space/functionality. You’ll need to create an account for some of them, but again that’s free.

Libre Office – I use my own laptop in the lab and as a result of that I don’t have some common software like Photoshop, Illustrator and most annoyingly, Microsoft Office. Rather than paying out of my nose for a productivity suite like Office, I chose to have a go at some open source alternatives. LibreOffice is an open source productivity suite that’s spent around 20 years in development, so it’s pretty stable. It comes with the same kind of programs as Office, a word processor, spreadsheets, presentation maker, drawing tools etc. It’s also compatible with MO as well, so you can open documents you created in program with the other. Migrating from Microsoft to LibreOffice was pretty easy and most of the layout and functionality is the same. I’ve been using this for a year or so now and I think whilst it still lacks the polish of Microsoft Office, it works just as well.

AlternativesGoogle Docs, laTEX (this is supposed to be specific for creating manuscripts)

Dropbox – I mentioned this in a comment on a previous post, but I’ll go into a little more detail here. Dropbox is basically a file syncronisation tool that you can download as a client program. Once installed, if you place a file in your Dropbox folder, it syncs it with your account so you can access that file from anywhere with an internet connection. It’s very easy to use and once you set up your Dropbox folder, you can share it with anyone. The syncronisation between folders on different computers is very fast, you can upload a file onto a shared Dropbox folder and within seconds the other person receives the file. This is very useful for collaborations or even just sharing data in a lab.

The servers they use to store files are very secure and you can create multiple sub-folders that you can share with various people. You get 2GB free storage but if you invite other people to share your folders or install it on another computer you get some extra storage.

AlternativesSugarsync

Mendeley – Mendeley is a web based reference manager that also has a desktop app you can download to organise PDFs and documents on your computer. The web app lets you build a library with an easy to use web importer that works as a plug-in to your browser. Mendeley also store pdfs on the (up to 500MB) and you can retrieve them from any computer or share them with other users by forming groups.

The Mendeley desktop app organises and indexed your PDFs that are stored on your computer. You can also annotate, highlight and add sticky notes to your files. As I begin to write my thesis, I’m finding this part increasingly useful. There is also a toolbar you can install in Microsoft Word or LibreOffice to cite papers whilst writing.

Unlike Endote, it’s free (although you can pay for more cloud storage) and unlike Papers, it’s a cross-platform tool (available for Windows, Mac and Linux), making it very useful for collaborations. I find the interface really easy to use and within half-hour of downloading it, I had most of my references stored on the desktop app. Also the ability to annotate and make notes on papers is proving to be invaluable.

Alternatives - Zotero

Reflect – This is a useful look-up tool when reading papers online. Basically, it’s a plugin for your browser that highlights proteins/molecules/biological concepts in any text. You can click on the highlighted text to show a pop-up window which displays some basic information such as what the molecule is, it’s role, structure and what it interacts with. The information displayed is community driven so for really obscure proteins and molecules there might not be a lot of information displayed, but the makers are keen on the community using it to edit and add more information.

Doodle – Doodle is a web-based time management tool that you can use to co-ordinate meetings. It does this by creating simple polls where everyone can vote on when they are free. You can use various calender programs like iCal, Microsoft Outlook or Google Calender to track dates and organise meetings with other people. I’ve never used it professionally, only with friends to organise some camping trips and it’s a pretty handy tool that saves on a lot of emails.

Alternatives -  Timebridge

OMERO –  OMERO is an microscopy image management tool created especially for scientists. It’s designed by the Open Microscopy Enviroment team which is based in multiple sites across the globe. Once you have an account set up and downloaded the programs, you can upload your images to a central server and process/analyse images and even make them ready for publication with a nice figure making tool. The Journal of Cell Biology has a data viewer based on OMERO that allows authors to upload images as they were acquired and users can look through z-stacks, time lapses and individual channels in these images.

If you have any tips for other useful freeware let us know in the comments section below.
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Comments
  1. Marsha Lucas says:
    Nice post! Very informative. I use a few of these already and will try some I just learned about today.


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  2. Nishal Patel says:
    Also I just found out that if you sign up to beta-test Dropbox’s photo uploader, they give you 5GB free!

    http://forums.dropbox.com/topic.php?id=53104


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  3. Christoph Budjan says:
    .. and another 16 GB free if you go through this:

    http://lifehacker.com/5854955/how-to-max-out-your-dropbox-referrals-with-google-adwords-for-free

    I’ve already tried it myself successfully and now have close to 20 GB of dropbox space.

    Don’t forget to upgrade to a student account to get 500 MB per referral (and increase your maximum free space limit).


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  4. Heather says:
    Excellent. I second Marsha’s comment.

    In theory there is Gimp to do what Photoshop does. But the learning curve is just as steep for me, and in the end I gave in and bought Photoshop. Some reflections and comments in that decision over here. But I still regret not having Linux on a work computer - they’re all hooked up to a microscope, or otherwise need to run software that otherwise is only written for Mac OS/Windows.


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    • Eva Amsen says:
      I found Photoshop easier to learn than Gimp. But now that I don’t have access to the lab copy of Photoshop anymore, I’m back to the confusing Gimp again. I don’t need it very often, which is not helping with the learning curve. It’s functional, but the interface is non-intuitive.


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