In this video, I introduce the concept of software-as-a-service, and discuss one system that uses this approach to maximize lab efficiency. The videos and the text cover mostly the same material, so you can choose whichever format you prefer – but make sure to check the end of the text here for something special I lined up in case you’re interested in using the system discussed.

In the last article I illustrated how you can gain a hypothetical $40k/yr for your research using a modest assumption that you can increase your overall efficiency by 20% for a lab operating on a budget of $200k/yr. In this post I’m going to show you one system that might help you accomplish that.

Let’s start by thinking about this scenario: you had a post-doc who published a paper five years ago.  Today, someone calls you up to ask for the cell line that he used and the protocols to grow it.

Where is it?  What state is it in?  How do you grow it?

Brushing off the dust

You could brush off the dust and hunt through stacks of old lab notebooks, trying to find information about his experiments.  Then once you find it, you’d have to go hunt through your freezers, and hope that you can find the original dishes, intelligibly labeled.
Think about how much time you might spend on a request like that.  In my own case, the answer is not pretty.  (In fact, I get a bit anxious even thinking about it).

There are all sorts of “little bleeds” like this, sapping time and money from your lab (and mine!).

The web has enabled a new way of handling these kinds of situations to stop the bleed. For the past few years I’ve been exploring “cloud-based” solutions for organizing lab activities.  Many have been useful, but most are generic business-focused solutions.  Much more recently, I’ve run across several solutions that are very specifically designed for science labs, and this got me curious.  Do they stack up?  Will they help make the lab run more efficiently?

The first one of those systems that I’d heard of early this year is BioKM by the company BioData.  I started playing around with a demo of the system last summer, and was sufficiently impressed to go a bit deeper with it.  The rest of this blog post dives into the system in more depth (as do the videos). I’ll say up front that I’m excited about the system and I’m putting it into place in my own lab, so the text may show a bit of that excitement…

Easy to use from the start

From my first experience with the system, I could tell that this was designed by a scientist for a scientist.  It is quite intuitive.  I had no trouble figuring out how to navigate through and see all the different aspects of my projects, data, supplies, and so on.

It did take me a while to figure out how powerful the linking feature is (more on that below), as it wasn’t immediately obvious how much could be done with that.  But once I figured that out, it is a “killer” feature.

The reason linking is so important is illustrated by the example I gave before about the request for a former post-doc’s cell lines. In a system like BioKM, responding to this request is pretty simple: you log in, navigate over to the “papers” section to find the published paper, and then see all of the items that are linked to the finished paper – the cell cultures, protocols, and reagents.  BioKM tracks location information (down to the individual well or test tube), so, as long as someone entered the information in the first place, you’ll pinpoint where the cultures are right away.  The protocols are also linked, so that when you send the sample off to your colleague, you can include a copy of the protocol.

Thinking about that makes me wish I had had such a system in place years ago!  I can think of several headaches that would have been spared.

Anyway, I’ve recently become an efficiency nut.  I used to be one of the most disorganized people on the planet, and the more I get organized, the more efficient that all my operations (lab and businesses) run.  Hopefully it is pretty clear to you too how tracking your supplies, materials, and protocols is so important if you want an efficient lab.

Drilling down into how BioKM might help accomplish this, it focuses on organizing five primary areas of your operations:

  1. Track your projects to hold people accountable, make sure they are on task and that they are operating efficiently. The interface has a full-featured group project tracking application where you can define a project (e.g. “Develop new HIV vaccine”) and then break that into milestones (e.g. “Determine the proteins involved in immune evasion” and “Determine the biological effects of mutations at the L42 locus”).  Each milestone is broken down into tasks, and you can set deadlines or goals for those that appear on the group calendar.  For each milestone, you can attach notes, experiments, and files.  You can delegate the tasks to individuals in your group, and track who is getting what done.  You can find out where the bottleneck is, and quickly move to overcome it.  This stuff is really important – by introducing project and milestone tracking in my own lab, we’ve seen a significant improvement in output.  Also, by implementing better tracking and accountability, you actually make your staff happier to work in your lab (that’s really important if you want them to be productive!).   They will feel more focused and clear on what they are supposed to be doing, rather than being stuck with the frustration of not knowing what to do next.
  2. Track your specimens – never wonder where they are again. Most of us working in or running biology labs create and/or operate with specimens (cell lines, animal lines, plants, etc) of one kind or another.  Even though these are often costly to develop or acquire, keeping track of them can be a real problem. This is especially true when people leave.  As we talked about with the former post-doc example, this is especially problematic when people leave your lab.  In our lab’s freezers we have stocks that are from people that left years ago, and with an impending move, I’m not sure how to deal with the problem.  I wish we’d had something like this to better track them.
  3. Increase your lab’s communication efficiency with the knowledgebase. The knowledgebase in BioData is designed to keep track of your papers, protocols, documents, and images.  If you’re like most labs, more than once you’ve tried to find a protocol developed by a former student or technician, and it was left on an old computer hard drive somewhere, or buried in a stack of lab notebooks.  If you’re lucky it only takes a few hours to find it.  If you’re unlucky, you have to re-create it from scratch.  I remember one case in particular of a paper that a postdoc had written and that we submitted before he moved on to a faculty job.  Later, when revisions had to be done to get it accepted, he was completely incommunicado due to being in New Orleans during Katrina.  He’d had to leave without his stuff or his computers, and was homeless!  So I had to piece together what he’d done, and re-create two figures from scratch to get the paper into shape.  That consumed several days of my time and tons of patience in trying to piece these things together.  I can only imagine the difference it would have made to have this all in one place at the time.It is clear that the BioKM system is designed to facilitate locating these kinds of documents centrally, so that you’ll be able to access them (or give access to them) immediately, anywhere you are.  When new images are acquired (e.g. from a microscope or gel), you can have a look at them so that you and your people can communicate and figure out what to do next.  This may take some habit re-setting for people in your lab (as I’ve gone through implementing a system like this), but the payoff can be big.  Next time you sit down to write a manuscript, you can immediately grab the relevant images and protocols to put into the paper. Yay for that.
  4. Track your gene, primer, RNA, and antibody sequences. Genes, primers, plasmids, antibodies – all of these have sequences that usually need to be stored for later use.  Storing them in flat file documents on your hard drive means that you’ll spend a lot more time hunting for them the next time you need them – and if your hard drive fails, they’re gone. Nothing drives me crazy more than when a critical sequence gets lost in a hard drive crash.  I’ve seen it happen. Biodata allows you to store sequences, then link them to other objects such as protocols, papers, or cultures.
  5. Use your supplies efficiently, and don’t run out. One of the challenges running a wet lab is keeping track of supplies such as reagents and enzymes, knowing when more needs to be ordered, when stocks are getting low (or out of date), and so on.  This is a part I’m really horrible at.  Just this one function can consume many hours per week.  BioKM has a module designed to optimize tracking of stocks and the vendors that you order from. It tracks quantities, costs, vendors, and the actual physical locations of your current stocks, and it can facilitate placing orders when stocks are low.  It can help eliminate redundancy, going in the direction of “lean” operations.  This is a good thing all around.

While it’s handy to have each of those individual tracking capabilities, the thing that is the most powerful about the system that linking thing I mentioned before.  It allows you to link all of your items together.  You can orchestrate and track complex experiments, having a protocol tied to the reagents and cultures, with milestones and tasks delegated to various people in the lab.  When it’s all done and distilled into a paper, that paper can be uploaded and linked to all the bits of information used to produce it.  I love this idea, and I hope you don’t mind if I repeat myself: I wish I’d had this kind of system in place years ago!  (My lab is about to undergo a big move, and the thought of figuring out where everything is – and what it is – scares me.  It could have been so much simpler if we’d had this system…)

As you can probably tell, I’m into this.  I think that this kind of tracking can save both time and money – but also sanity.

I’d like to say a word about cost.  BioKM isn’t free after the first 30 days, it is a paid subscription (you can get started very inexpensively, but for a big lab the price goes up).  While I’m very much in favor of free solutions, sometimes (often times!) free solutions come with a big cost: your time.  I’ve had plenty of “free” software that sapped days, weeks, or months to get up and running.  I contacted BioData while writing this post, and they reminded me about the responsive support they provide people to get up and running. I hadn’t thought about it, because I didn’t need any support to get going with the system.  But it is nice to know that it is there.  Also, when I talked to BioData, they offered a coupon code to help with the cost a bit – see the end of this post for that.

In studying successful people in all walks of life, this is one thing that they do: they realize that time is the very most precious resource they have.  You can get more money, but not more time.  This realization was slow to dawn on me, but it has resulted in tremendous gains in my productivity.  My point is that when you think about whether the cost of a system like this is worth it or not, I do hope you’ll include your time costs for the alternatives (such as doing nothing or implementing a free solution).

One major deficiency (but it is common to all organizational systems)

I have to be realistic about one big deficiency of all such systems: you have to get in the habit of using it, and so do your people. Without that habit, it will be useless to you. Depending on you and your staff’s natural inclination towards such things, this could be a minor or a major challenge.

In my lab, we’ve experimented with various organizational systems for our data and projects, and I’ve found that, following an initial burst of use, enthusiasm wears off, and some people will stop using a system, unless prodded to do so.

In general, I’ve found that it takes 20-40 days of doing something regularly to make it into a habit.  Personally, the idea of making my lab a lot more efficient is worth the effort to make that into a habit for myself and the staff.  But I just want you to be aware that it takes some time and focus to do.

Here I show a short overview of the system in case you want to see how it works:

In this video, I give an overview of the BioKM system.  At the end of the video I mention that the company has offered a discount for Morgan On Science readers by using the coupon code “SciFoundry”  The company contacted me after seeing the video and reminded me that the discount is 15% for the first year, rather than 10%.

Storing data externally

The one issue that bears discussion is the storage of your data on external servers.  The positive in this is that you don’t have to worry about maintenance, backups, crashed hard drives, and etc.  That worrying is done by the people that maintain the servers at the other end.  The two potential downsides that arise over this are data security and data recoverability.  On the data security end, I’m not too concerned because BioKM uses the https encrypted protocol for communications – the same one used by credit card companies.  Is it perfect? No, but neither is a computer sitting in a lab (which can be hacked or stolen – especially if it is a laptop).

On the point of whether your data is recoverable, BioKM does have an export feature.  To ameliorate any concerns about this, I’m going to set someone up in my lab to do an export once every two weeks or so, just as a precautionary measure.  Then I’ll store those export data sets on a backup drive somewhere secure.  That way you make sure to always have a recent copy of your data both locally and on the BioKM servers.

To wrap up, I like it a lot.  While there are some other great systems for doing some of what this does, this is the first I’ve encountered that deals with both the project management side and the supplies/reagents/stocks side of things so well.

Enjoy getting organized, and stay tuned for overviews of other organizational systems.


ps – make sure to leave a comment with your thoughts about implementing such a system in your own lab. Do you think it would help?

    4 replies to "More research money without more grants, part II"

    • Alexandra

      It would be useful to know how this system compares to the one of custom-made FileMaker Pro databases already used by several labs. Thanks.

      • morgan

        Hi Alexandra,
        It is hard for me to make the comparison since I don’t have access to the custom-made databases. However, my lab and my team does have a lot of experience developing large databases for managing data (we have some publications on this), and I think that developing something as rich as a system like BioData – and maintaining it – is not a trivial task.
        That said, if the labs that have the custom filemaker databases are totally happy with what they’ve got, there’s probably no reason to change. But if someone were to be starting from scratch – especially someone without a lot of computing expertise – I’d really recommend some kind of solution like BioData (there are others too, and it doesn’t matter as much which system as much as just getting going with the concept of organizing your lab using some system).

    • Stephen H. Devoto

      We use a custom FileMaker Pro database that dates back to the founding of the lab. Its functionality is fantastic when people diligently enter information, and purchasing and fish lines databases are incredibly useful. On the other hand, our oligos, plasmids, and probes databases are not.
      As long as data entry is the ‘limiting reagent’, I see no benefit from paying money for a new organizing system.

      • morgan

        Hey, that sounds like a great system. I agree, if you already have a system in place that works, no need to do something like this. I think BioKM is designed for those who don’t already have a satisfactory system in place, and who want to get up and running quickly. But regardless of which system you are using, I think it is important to use some system (in house or not).
        Do you share your database structure for others to use? I’d be happy to post a link here if you have one.

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