Data Questions: Who Can Help?

Discussions about data seem to be everywhere.  For evidence of this, look at recent discussions of big data, calls for increasing cyber-infrastructure for data, data management requirements by funders, and data sharing requirements by journals.  Given all of this discussion, researchers are (or should be) considering how to handle their own data for both the long term and the short term.

Admit it: You can’t help yourself. You need the expertise of others! The Four Tops knew it. Image from (click for more). Check out this live performance of “I can’t help myself”:

The popularity of discussions about data is good and bad for the average researcher.  

Let’s start with the bad first: it means researchers are now, more than ever, responsible for being good data stewards (before commenting that this “isn’t a bad thing!!” read on).  Gone are the days when you could manage your data in-house, with no worries that others might notice your terrible file naming schemes or scoff at the color coding system in your spreadsheets.  With increasing requirements for managing and sharing data, researchers should be careful to construct their datasets and perform their analyses knowing that they will have to share those files eventually.  This means that researchers need to learn a bit about best practices for data management and invest some time in creating data management plans that go beyond simply funder requirements (which are NOT adequate for actually properly managing your data – see next week’s blog post for more).

Arguably, the “bad” I mention above is not actually bad at all.  Speaking from the point of view of a researcher, however, anything that requires more demands on your time can be taxing.  Moving on to the good: all of this attention being given to data stewardship means that there are lots of places to go for help and guidance.  You aren’t in this alone, researchers.  In previous posts I’ve written about the stubbornness of scientists and our inherent inability to believe that someone might be able us.  In the case of data management and related topics, it will pay off in the long run to put aside your ego and ask for help.  Who? Here are a few ideas:

  1. Librarians.  I’ve blogged about how great and under-used academic libraries and librarians tend to be, but it is worth mentioning again.  Librarians are very knowledgeable about information.  Yes, your information is special. No, no one can possibly understand how great/complex/important/nuanced your data set is.  But I promise you will learn something if you go hang out with a librarian.  Since my entry into the libraries community, I have found that librarians are great listeners.  They will actively listen while you to babble on endlessly about your awesome data and project, and then provide you with insight that only someone from the outside might provide.  Bonus: many librarians are active in the digital data landscape, and therefore are likely to be able to guide you towards helpful resources for scientific data management.
  2. Data Centers/repositories.  If you have never submitted data to a data center for archiving, you will soon.  Calls for sharing data publicly will only get louder in the next few years, from funders, journals, and institutions interested in maximizing their investment and increasing credibility.  Although you might be just hearing of data centers’ existence, they have been around for a long time and have been thinking about how to organize and manage data.  How to pick a data center? A wonderful searchable database of repositories is available at Once you zero in on a data center that’s appropriate for your particular data set, contact them.  They will have advice on all kinds of useful stuff, including metadata, file formats, and getting persistent identifiers for your data.
  3. Publishers and Funders.  Although they wouldn’t be my first resource for topics related to data, many publishers and funders are increasingly providing guidance, help text, and links to resources that might help you in your quest for improved data stewardship.

My final takeaway is this: researchers, you aren’t in this alone. There is lots of support available for those humble enough to accept it.

Workflows Part II: Formal

cummerbund pic

Nothing says formal like a sequined cummerbund and matching bow tie. From (click the pic for more)

In my last blog post, I provided an overview of scientific workflows in general. I also covered the basics of informal workflows, i.e. flow charts and commented scripts.  Well put away the tuxedo t-shirt and pull out your cummerbund and bow tie, folks, because we are moving on to formal workflow systems.

A formal workflow (let’s call them FW) is essentially an “analytical pipeline” that takes data in one end and spits out results on the other.  The major difference between FW and commented scripts (one example of informal workflows) is that FW can be implemented in different software systems.  A commented R script for estimating parameters works for R, but what about those simulations you need to run in MATLAB afterward?  Saving the outputs from one program, importing them into another, and continuing analysis there is a very common practice in modern science.

So how do you link together multiple software systems automatically? You have two options: become one of those geniuses that use the command line for all of your analyses, or use a FW software system developed by one of those geniuses.  The former requires a level of expertise that many (most?) Earth, environmental, and ecological scientists do not possess, myself included.  It involves writing code that will access different software programs on your machine, load data into them, perform analyses, save results, and use those results as input for a completely different set of analyses, often using a different software program.  FW are often called “executable workflows” because they are a way for you to push only one button (e.g., enter) and obtain your results.

What about FW software systems? These are a bit more accessible for the average scientist.  FW software has been around for about 10 years, with the first user-friendly(ish) breakthrough being the Kepler Workflow System.  Kepler was developed with researchers in mind, and allows the user to drag and drop chunks of analytical tasks into a window.  The user can indicate which data files should be used as inputs and where the outputs should be sent, connecting the analytical tasks with arrows.  Kepler is still in a beta version, and most researchers will find the work required to set up a workflow prohibitive.

Groups that have managed to incorporate workflows into their community of sharing are genomicists; this is because they tend to have predictable data as inputs, with a comparatively small set of analyses performed on those data.  Interestingly, a social networking site has grown up around genomicists’ use workflows called myExperiment, where researchers can share workflows, download others’ workflows, and comment on those that they have tried.

The benefits of FW are the each step in the analytical pipeline, including any parameters or requirements, is formally recorded.  This means that researchers can reuse both individual steps (e.g., the data cleaning step in R or the maximum likelihood estimation in MATLAB), as well as the overall workflow).  Analyses can be re-run much more quickly, and repetitive tasks can be automated to reduce chances for manual error.  Because the workflow can be saved and re-used, it is a great way to ensure reproducibility and transparency in the scientific process.

Although Kepler is not in wide use, it is a great example of something that will likely become common place in the researcher’s toolbox over the next decade.  Other FW software includes Taverna, VisTrails, and Pegasus – all with varying levels of user-friendliness and varied communities of use.  As the complexity of analyses and the variety of software systems used by scientists continues to increase, FW are going to become a more common part of the research process.  Perhaps more importantly, it is likely that funders will start requiring the archiving of FW alongside data to ensure accountability, reproducibility, and to promote reuse.

A few resources for more info: