Python For Handling 96-Well Plate Data and Automation

book-graphics.005There’s hardly a life science lab you can walk into these days, without seeing a ton of 96-well plates and instruments that read and handle them. That’s why we’ve dedicated an entire chapter of our forthcoming book Python For The Life Sciences, to the humble 96-well plate.

The chapter introduces the use of Python for handling laboratory assay plates of many different sizes and configurations. It shows the reader how to read plate assay data from files formatted as comma-separated values (CSV), how to implement basic row and column computations, how to plot multi-well plates with the wells color-coded by their properties, and even how to implement the high level code necessary for driving instruments and robots through devices like Arduinos.

And this is just one of about 20 chapters designed to introduce the life scientist who wants to learn how to code, to the wonderful and versatile Python programming language.

Almost all of the code and examples in the book are biology-based and in addition to teaching the Python programming language, the book aims to inspire the life scientist reader to bring the power of computation to his or her research, by demonstrating the application of Python using real-world examples from across a wide range of biological research disciplines.

The book includes code and examples covering next-generation sequencing, molecular modeling, biomarkers, systems biology, chemical kinetics, population dynamics, evolution and much more.

Python For The Life Sciences should be available as an eBook this fall (2016), so if you’re a life scientist interested in bringing a computational skill set to your research and your career, visit the book’s web page and sign up to our (no spam) mailing list for updates about the book’s progress and publication.

© The Digital Biologist

Symposium On The Future Of Research 2015

6a00e553e3a603883401b7c7e2bdcf970b (1)After enduring years of steady erosion of their funding, pay, career opportunities and work/life balance, it’s great to see researchers taking things into their own hands and getting behind a truly grassroots organization like Future Of Research (FOR) that was founded in October 2014 to address these issues. I was fortunate enough to be able to attend the 2015 symposium and what follows are my thoughts on what I heard there and where things stand for academic researchers, a year on from the launch of FOR.

I’m not going to reproduce all of the sombre statistics that were presented, illustrating the extent to which the working conditions for academic researchers in the U.S. have deteriorated under a system that rewards the worst kind of aggressive individualism while paying lip service to ideas like collaboration and collective effort. And all of this while trying to squeeze more and more out of researchers in return for low pay, low status and poor career opportunities.

The current crisis in academic research in the U.S. has been years in the making and is already well documented

To a very large extent, it can also be viewed as the unfortunate sequela of a much broader social crisis that we are currently witnessing in the U.S.

Let me state from the outset that the opinions that follow are entirely my own. I have no affiliation with the Future of Research. I would say that for me, the 2015 FOR Symposium was very enjoyable for the most part but also something of a disappointment, mainly for the following reason: Despite the general consensus that the current academic research system is broken and unsustainable, the great majority of the content presented at the symposium focused upon how researchers can optimize their career prospects within this broken system, rather than trying to change the system or seek alternatives to it.

For me, the 2015 symposium was less about the “Future Of Research” than it was about how to survive the current crisis.

This is not to say that any of this isn’t well-intentioned or laudable, but I feel that it misses the essential point of trying to forge a better future for researchers. There is already an entire industry of recruiters, coaches and consultants built around helping researchers navigate the current system, and I felt that recycling this material, however well-intentioned, was not really in the spirit of FOR’s stated goals of improving the scientific endeavor.

Again, it’s important to note that this is only my personal perspective on the symposium, based largely upon my own expectations. The conversation in which FOR is engaging the research community is an important one and there are undoubtedly many possible paths to take, depending upon what each of us feels represents a real solution to the crisis. I may differ with the FOR organizers over the content and approach of  their 2015 symposium, but not over the substance of their mission, which I support wholeheartedly.

I would also like to make another observation that I feel is directly germane to the choices made by the organizers of the FOR symposium. My overwhelming impression of the general sentiment amongst the academics who were present, is one of helplessness and disempowerment; a feeling that there is an academic research  ‘establishment’ composed of a relatively select group of gatekeepers who hold the keys to everything, and without whose help and blessing, nothing meaningful can be done to improve the current situation. From such a perspective, it is much easier to contemplate seeking permission to act within the constraints of the system (and presumably with the approbation of its establishment), rather than taking the much more challenging path of trying to change the system.

I do not accept the argument that one researcher voiced to me, that this is just a kind of pragmatic wisdom that offers a better chance of success because it’s based upon a more realistic perception of how things are.

These establishment gatekeepers – the academic journals, the NIH, college admission and tenure committees etc. etc. etc. dominated the conversation either in absentia, or in the case of the journal publishers, actually in the room. I have to confess that I was somewhat perplexed by the organizers’ decision to give a platform to the publisher Cell Press. As a corporation that takes publicly-funded research and puts a paywall around the results, they are much more a part of the current problem than they are any part of its solution. They also play a big role in the kind of self-fulfilling academic career inequalities born of insidious metrics like ‘impact factors’ and the awful ‘publish or perish’ mentality that can make academic research such a miserable experience, even for many really good and gifted researchers.

Even worse, most of the publishing industry panelists on the stage proceeded to school the attendees on their expectations for how manuscripts should be prepared and submitted, while disingenuously engaging in the charade that this was all to the benefit of the researchers (yes, let’s add ‘unpaid editor’ to the list of the overworked and poorly paid scientist’s responsibilities). Even the research faculty panelists who sat on the stage with the publishers, wasted little time in perpetuating the notion that there is really only one path to success in academic research and that it involves playing by the publishers’ rules.

Despite the presence of The Winnower and Faculty Of 1000 on the panel, who were beacons of hope in this otherwise rather depressing portion of the symposium, it was disheartening to see the academic publishing status quo going relatively unchallenged. Indeed, this part of the program seemed to be a thinly veiled message from the traditional publishers to all present, that this is just how things are and you  really need to get with the program if you’re to have any chance of success in your academic career. All of this passing I would add, with little or no serious discussion of other, better ways to do things.

status quo: 1, alternatives: 0

For all of the polite acceptance of the way things are and willingness to ‘play nice’ with it, there were one or two moments during the symposium in which some of the braver souls did step up and make impassioned pleas for something better – for example (and I’m paraphrasing): “How can we change things so that academic research is no longer a system of abuse?” and:  “How are postdocs supposed to start a family when their compensation during what would be their child-rearing years, is so dismally low that it essentially excludes the possibility?”

I was really horrified when a tenured faculty member on the panel actually suggested that this latter issue is not really a problem since the postdoc (a woman in this case) always has the option to leave academia and find a career path more conducive to starting a family.

Really?

After hearing earlier from that same faculty member that academic research needs to attract and retain “the brightest and the best”, we should probably append the caveat “so long as they don’t want to start a family”.

Another tenured faculty member on the panel dismissed the postdocs’ grievances by suggesting that the whole sorry state of affairs was just the result of the fact that we live in a capitalist society with free markets (and therefore, that we should presumably just accept things the way they are).

status quo: 10, alternatives: 0

Start to see a theme here?

It has been my experience that it is generally a waste of time to make an appeal to change the system, to those who have been raised up by the system and who are its beneficiaries. This is what drives my overwhelming feeling about what could be done to improve things for researchers and now if you’ll bear with me, I would like to connect the dots that integrate this idea with an issue raised in one of the more interesting portions of the symposium – the panel on diversity.

As one of the diversity panel rightly pointed out (and again, I’m paraphrasing here), by the time you’re considering diversity at the graduate school or postdoctoral level, you’re already at the tip of a huge iceberg beneath which much of the diversity race has already been run. The inequalities start at a very young age in the public schools and whether you’re a woman, a racial minority, or gay – by the time you get to the research level, the number of you still left in the race, has already been greatly depleted by years of systematic bias. How do you even start to address the diversity issue in your research department when as one panelist recounted, only 1 faculty applicant in 200 is a minority? For sure you can and should do everything in your power support diversity at this level, but sadly, much of the damage is being done long before the graduate school, postdoctoral or faculty hiring process.

But here’s where we can connect the dots with regard to the current situation in academic research and the fears of many who participate in it. One of the diversity panelists (a woman) really nailed the crux of the issue when she said that her boss, an older, white male, had certain expectations for the way that a female colleague should behave and express herself. Remaining silent with regard to her (very legitimate) grievances on how she was being treated as a woman in the workplace was essentially ‘rewarded’, but of course, under such circumstances nothing changes for the better. Airing those grievances on the other hand, was considered unseemly and overly aggressive in a way that it would not have been if she were a man. This behavior would also most likely result in the proverbial blot on her career copybook – an awful Catch-22 if ever there was one.

Which brings me to what I consider to be the crux of the issue for the research crisis.

We really need to be exploring alternatives to the current system rather than just trying to reform it. 

It’s sad but true I think, that the great majority of those ‘old, white guys’* alluded to by the female diversity panelist, who are in positions of authority and influence, are just not going to substantively help in any effort to dismantle what has gotten them (and keeps them) where they are. Now granted that this is an extreme analogy, but imagine the starving workers in pre-revolutionary St Petersburg, knocking on the Russian tsar’s palace door and politely asking that he and his nobles please address the current inequalities that are keeping them in poverty (as it turns out, this was in effect exactly what they did, and the response was brutal).

To be absolutely clear, I’m trying to make a point here – maybe with my tongue very firmly in my cheek, but a real point nonetheless – and of course I’m not advocating any kind of bloody revolution. But the current situation for scientific research is grave and I believe that what it does call for are the kind of alternatives that might be termed ‘revolutionary’ – revolutionary in the way that YouTube is transforming communication and self-expression – revolutionary in the way that Kickstarter is transforming the funding of business and the arts.

Even as we speak, there are already those who have taken the first steps into a new model of scientific research, both in academia and in industry. They are pioneers characterized by a willingness to look outside the bounds of the current model, many of whose leaders and influencers are all too eager to tell us that this is still the only game in town.

I firmly believe that it is not.

*Disclaimer: The author of this article is also an old, white guy, but of the kind with neither authority nor influence. You can therefore, quite safely tell him to go jump in a lake if you disagree with him, without fear of any damaging consequences for your career 🙂

© The Digital Biologist