Wednesday, May 28, 2014

Indispensable Software for a Biologist

I spend a lot of time on the computer, particularly analyzing data, writing grants and papers, and otherwise looking up information online to help me figure out the solution to a problem or set up an experiment.  

Every now and again, I pause and gaze in amazement at how much I depend on technology to do my job efficiently and correctly.  This is not just research technology like fancy microscopes and lab equipment.  This extends to computer programs, too.  We become very dependent on certain programs to fill certain roles, and I was thinking about the more important pieces of software that I would not want to be without.  

Inspired by that, I thought I would make a list of my five most useful and most used pieces of software in various categories, both as a recommendation and review as well as a "thank you" to the developers for contributing to making my life easier and more efficient.  This list will not come as a surprise to some other scientists, but some people might find it interesting or useful.  

Here we go:     

1) Data Analysis/Statistics/Graphing: GraphPad Prism

GraphPad Prism is one of the most user-friendly programs I have ever experienced.  It can be used to perform both fairly complicated statistical tests as well as simple Student's t tests.  It is intuitive, and the helpful resources on the GraphPad website are amazing not only in terms of telling you how GraphPad works but in teaching you about statistics in general.  

Statistical analysis is something I find that biomedical scientists (including myself) are often poorly educated about and have to learn via first-hand experience, often leading to statistical mistakes that can affect the validity of a papers conclusions (you can read about that here or here).  While nothing beats experienced colleagues or the help of a real biostatistician, you can gain a great foundation in biostatistics by using the GraphPad website and reading the book Intuitive Biostatistics by GraphPad founder Harvey Motulsky.  

I didn't discover Prism until I was a postdoc.  I really wish I had it while I was a PhD student, but better late than never.  I can't recommend it enough, even though it is a bit pricey.  Everyone that I know that has ever used it loves it.          

My runner-up in this category is IgorPro from Wavemetrics.  In my PhD lab, we had a joke.  If there was anything that needed to be done, we would say "just write an Igor macro.  Igor can do anything."  That joke is not too far off from the truth.  Igor really can do anything from statistical tests, data transformation, image analysis, etc.  Thankfully we had someone in the lab who was excellent at writing Igor macros, and many times I turned to him to help me solve an analysis problem or automate an analysis.  

The learning curve for Igor is as steep as a cliff, but it remains one of the most powerful software programs I've ever seen.  Coupled with the active experienced members of the user-base who write and shares macros with each other (much like ImageJ below), and you really can do anything with Igor.  I don't think I'll use it much  now that I have GraphPad, but the ability to automate analyses (including image analyses) in Igor means that someday I may need to come back to it.       

2) Reference Management:  EndNote 

When you are writing a review paper that might have anywhere from 100-200 references or more, you need dedicated software to keep track of these references and automatically re-order numbered bibliographies after you rearrange the text.  I use EndNote from Thompson Reuters.  I don't know how I could be productive at all without EndNote and its ability to insert references directly into MS Word as well as to quickly import reference data from PubMed, change bibliography citation format, and re-order references at will.  I've also used RefMan before, but found it to be slower and slightly less intuitive.  I prefer EndNote, but a lot of this may just be due to habit.  I would, however, use RefMan long before I would use any of the freeware programs I have tried.  This is one category where freeware reference programs just can't hold a candle either of the fancy brand names.  

3) Image Analysis:  ImageJ

Here, however, is a category where the freeware program dominates.  ImageJ is much like Igor Pro in the sense that you can do anything with ImageJ, at least in terms of image analysis.  Originally descended from NIH Image, ImageJ is a public domain (in other words, free and freely editable) java-based program developed and maintained by Wayne Rasband of the US National Institutes of Health (NIH).  ImageJ has an extensive collection of plugins written by an army of user-programmers that allow it to do almost any image analysis processing you can think of.  I've spent a lot of time using ImageJ, and I actually learned a large portion of what I know about image analysis from reading posts on the ImageJ mailing list and associated archives.  The mailing list was a really valuable resource while I was doing my PhD.    

My three favorite ImageJ bundles (which include various sets of plugins) are the McMaster Biophotonics ImageJ, FIJI, and Micromanager (µManager).  I use the McMaster and FIJI version to do different post-aquisition analyses, while I use Micromanager to run a Nikon TE2000E microscope for wide-field fluorescence imaging.  My lab inherited a microscope that didn't have the associated software with it (the computer had died and we the discs had disappeared), and at the time we didn't have the cash to buy imaging software, so I gave Micromanager a try.  I've been pleasantly surprised by using it as well as the ease of setting it up.

Not only is ImageJ great for science, but it can also work for a lot of other uses.  Amateur photographers or other artists could use ImageJ to changing image file formats, change bit-depth of images, turning image stacks into videos, adjusting color balances and/or brightness/contrast settings, etc. etc.  A dedicated open-source photography program (like GIMP) would do it more easily, but ImageJ can do quite a lot in a pinch.           

4) Cloud Storage Syncing Software (Dropbox/Box/Copy/OneDrive/Google Drive)

Cloud computing software has really changed the way I work.  I carry three flash drives with me everyday (a 32GB, a 16GB, and an 8 GB), used mostly for transferring sometimes-large files from computers hooked up to microscopes or other instruments.  I used to carry more, and it was a pain to remember what files were saved to which drive if I forgot to immediately transfer them to my work computer.   Now, if a computer is connected to the internet, I can upload smaller files directly to cloud storage.    

Cloud storage allows me to access them on any computer I want to log in to, but moreover the free downloadable programs from these companies allow automatic syncing of my files and allows me to work with files saved locally to my Dropbox, Google Drive, etc. folders and not have to worry about backing them up to the cloud.  It makes me really happy that my important work files (kept in these folders) are backed up almost instantaneously and it doesn't depend on me needing to remember.  If my computer hard drive crashes, I'm covered for the most part.  Because I'm cheap, I use the free versions of multiple cloud services, but that gives me quite a bit of storage space to utilize.  The only one I pay for is OneDrive, which comes with my Office 365 subscription, which I'll talk about below.       

5) Word Processing/Presentations:  Microsoft Office 

Last, but certainly not least, the most important software package I use is Microsoft Office, specifically Word, Excel, and Powerpoint.  I'm sure that many of you reading this blog likewise depend on Office daily.  Scientists are no different in this regard.          

Writing papers and grants and making presentations for seminars and classes are a large part of what scientists do.  You need solid and reliable programs for both document preparation and presentations.  Additionally, a spreadsheet program is indispensable for keeping track of data, and a lot of data analysis can be done in Excel (Student's t tests, linear regression, etc.).  Moreover, a lot of scientific instruments (e.g., colorimetric plate readers and microscopes) have software that can output in tab-delimited text formats that Excel can easily read.      

There are other office suites besides Microsofts Office.  Some people like using Google Docs, which has the benefit of being free, while some people like Apple's iWork, which is much less expensive than Office and quite pretty and well designed.  I've played around with Keynote quite a bit on and off over the last few years.  There are some things that Keynote even does better than Powerpoint (and vice verse).  Overall, though, I prefer Office, despite the fact that I am generally a huge Apple fan.

Office just seems more user friendly and more stable to me, particularly when working with large documents with lots of inserted images, like when preparing academic papers for publication.  I'm sure that some of my Office preference, though, is likely habit.  With every piece of software, you learn more tricks and shortcuts over time, and I've just spent hours and hours of my life using Word, Powerpoint, and Excel.  At this point, they just to work pretty intuitively to me.         

However, regardless of what office suite you prefer, I've found that more often than not, almost everyone that you will collaborate with is going to send you files formatted in Word's .doc/.docx format and presentations in Powerpoint .ppt/.pptx format.  Microsoft Office is more often than not what other people are using; it is really the industry standard.  Frequently you need to open other people's documents to edit them or otherwise modify them and send them back.  This often involves using "track changes," which is one place that other office suites get particularly hung up on in terms of compatibility.  I've found that the only way to ensure 100% compatibility and transferability is to use Office.  

I remember the days (maybe 10 years ago) when you had to worry about PC vs Mac compatibility issues even within Office, but thankfully those days are long gone.  I've taken many .doc/.docx and .ppt/.pptx files from Mac to PC and back to Mac, and there are really no longer any problems with this that I can tell.
I keep iPad Office the front page of my iPad home screen.
I just want to throw out a quick shout-out to how much I am enjoying Office on my iPad since it was released in March.  I absolutely hate that I can't just buy it and need to sign up for the Office 365 subscription in order to fully use it, but it works marvelously and seems to be fully compatible with the desktop version I use on my Mac.  I already own copies of Office for both PC and Mac, and would prefer just to buy an iPad version without a subscription that seems excessively costly ($100/year).   

I originally signed up for Office 365 month-by-month in order to test it out, but I haven't canceled it because it works so well, and I've been using it quite a bit.  Coupled with my Logitech keyboard cover, it turns my iPad into something on which I can get some serious work done when I need to travel and don't want to take my heavier laptop with me.  I also really like the ability to show Powerpoint presentations from my iPad without any screw ups.  I've tried opening my Powerpoint presentations in Keynote, Quickoffice, and Polaris Office, and (if they open them at all without freezing up) there are always font or animation issues that require a lengthy time to edit as well as often a lag when transitioning between slides.  Cloud-based solutions like CloudOn work well to show Powerpoint presentations but require an active internet connection.  Only the actual bonafide Powerpoint app allows me to download a copy of my presentation to my iPad and show it flawlessly offline.  It is also faster, with minimal lag-time between slides with complex vector (pdf) graphic diagrams.  Part of my lag issues are due to the fact that I am using an iPad 3 from 2012 (my iPhone 5S actually opens presentations more quickly), but I appreciate that the bona fide Powerpoint app runs more efficiently and minimizes the issue.                      

6) Bonus program that I used to really love: ACD Canvas

The program that I miss the most is ACD Canvas.  The best way I can describe Canvas is a combination of Adobe Photoshop and Illustrator put into one super-useful and super-powerful technical drawing and layout-generating software.  I used to love that program, but Canvas stopped being developed for Mac after version 10 (X), and version X doesn't run on the latest versions of OSX which don't support PowerPC programs due to the lack of inclusion of Rosetta.  Thus, I try not to use Canvas very much anymore.  Just in case I need to open an old Canvas file that I have, I have an G4 Mac Powerbook from 2004 that still has OSX Snow Leopard Canvas installed on it (and still runs remarkably well despite some yellow spotty screen issues).  ACD still produces new PC versions, but overall I've replaced Canvas in my life with a combination of Powerpoint and GraphPad.  However, last year it was announced that we might have a new Mac version of Canvas in 2014.  I'm interested to see how that goes.      


It can be quite scary how much we depend on technology, including software that is often quite expensive.  However, to compete as a scientist, you need to be able to perform the proper types of analyses or make graphs and figures that look presentable and attractive.  A lot of science is simple marketing and communication.  It doesn't matter how good your data are if they aren't presented properly so people can understand them or if your conclusions are invalid because something you said was significant is not really significant (or vice verse).  The programs above have helped me a lot over the years.  

Text content for this post is ©2014 R.J. Lee, but the logos are the properties of the respective companies that own the software described.  Since I am reviewing these products favorably and with no commercial conflicts of interest (i.e., nobody is paying me), I assume that they don't mind that I am using their logos for this purpose.    


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