Managing samples in an electronic lab notebook
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Managing samples in an electronic lab notebook



Talk on how to manage samples in an electronic lab notebook given a Bioconference Live

Talk on how to manage samples in an electronic lab notebook given a Bioconference Live



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  • Hello everyone, and welcome to this Bioconference Live presentation on managing samples in an electronic lab notebook. My name is Rory Macneil, and I’m from Axiope. A quick disclaimer at the start. We provide an electronic lab notebook that includes a sample management capability. So I guess you could say I’’m an evangelist for managing samples in an integrated framework along with your experimental data! This is intended to be a practical, hands on session, so I’m going to show you in the last half of the presentation how you can manage samples and experimental data in our eCAT ELN. Before I do that I’m going to take a step back and set the scene by taking a look at how labs are currently managing their data and how this fits into their research and publishing workflows. Please fire away with questions at any time during the presentation. I may respond to a question as it comes in, or if it looks as if it’s going to interrupt the flow I will hold off and answer the question in the Q&A session at the end. If anyone would like to identify yourself and let me know what your particular interest in the presentation is, that would be great. I’ll try to make sure I cover things in a way that makes it relevant to your interest.
  • So, here’s a quick overview of what we’re going to cover today. I’ll start with a look at how the way we’re using information is changing, in and out of the lab. That makes an interesting contrast to how labs are dealing with experimental data and sample data, which is largely in the same way they’ve always done. Then we’ll examine the benefits from dealing with experimental data and sample data in an integrated framework. And we’ll conclude by learning how to do this in practice, with the eCAT electronic lab notebook, which includes a sample management system.
  • Changes in the way we communicate are impacting all of us. Scientists are no exception. Scientists use online communication tools like Facebook and Twitter in their personal lives. And a growing number of scientists are beginning to use them, and blogs, in doing and communicating science.
  • The way labs manage their information is also changing. Many labs use wikis to share general information like meeting notes, schedules and protocols. And Google Docs has become popular for sharing documentations and presentations. So people are becoming comfortable with the using the kinds of web-based communication and collaboration techniques they are adopting outside the lab in the lab environment.
  • But when is comes to the heart of the experimental process, dealing with experimental data and samples, things have hardly changed. The paper lab notebook is still the dominant place for documenting experiments, and information about what’s inside the freezer is still usually maintained in a series of spreadsheets. So, the enhanced information recording and communication possibilities the web is opening up are going largely unutilized by labs in their core research activities.
  • As I’’ll describe in a moment, there are now tools that allow labs to take full advantage of these new web capabilities, tools which handle both experimental data and sample data in a single integrated environment. As background to that, let’s ask why you would want to adopt an integrated approach in the first place. Here are six compelling reasons.
  • First, keeping track of your samples in a unified, searchable database leads to a massive improvements in the ability and ease of finding out about where samples are stored, what the number and status of aliquots is, etc.
  • Second, because you can link information about samples to the experiments in which the samples are used, you get a visual representation of the relationship. It’s also an electronic, and searchable link.
  • Third, these links enhance the quality of your experiments. You are more likely to spot errors early on in the experiment, and finding the aliquot and its history is now much easier, making retrospective checking a piece of cake rather than a frantic, stress-filled search.
  • Currently to find something that happened in an experiment or a series of linked experiments you probably have to look back through a series of labbooks of one or more lab members, and to locate a sample you have to look at multiple spreadsheets which may have different formats and entries from many current and former lab members. It can be like looking for a needle in a haystack. An electronic lab notebook with a sample management capability lets you easily locate any sample and any piece of experimental data entered by any current or previous lab member, and view it in a whole variety of contexts, from a single experiment or multiple experiments, to the set of samples kept in a particular freezer.
  • Improved experimental results and more efficient documenting of experiments means you can do more experiments, more quickly, and of a higher quality. And that in turn means better quality publications and quicker preparation of grant proposals. So you won’t end up like Snoopy!
  • You may not have thought much about it, but lab freezers use a lot of energy and are costly. For example, UC Davis estimates that it’s energy and maintenance costs for ultra-low temperature freezers, not counting refrigerators and standard freezers, are estimated to be over $1 million a year. Each of its 1,000 ultra-low temperature freezers at Davis uses the same amount of electricity as a large household (around 20 kilowatt-hours a day). It was numbers like these that stimulated Davis to start the Freezer Challenge, an initiative involving six universities competing to manage their samples more efficiently.
  • So, there are a lot of important benefits to integrated management of samples and experimental data. But is it possible today?
  • The answer is yes! In the remainder of today’s presentation I am going to take you through a specific example of managing samples in an electronic lab notebook called eCAT. From this hands on example you can see that it is now quite possible to manage samples and experimental together. Moreover, it’s not hard and does not require any special technical expertise. It’s quite feasible even for the run of the mill technophobe who hates software and thinks every moment spent at the computer is a distraction from time spent at the bench!
  • eCAT shows you the samples you have in your freezer boxes, and keeps their details private from other users. You can do all the things you’d expect to be able to do with samples, like aliquot them and check them in and out of freezers. You can set alerts on volume remaining, vial count, expiration date, and the number of freeze-thaw cycles. If you have aliquots listed on a spreadsheet, they will import straight into eCAT, or you can edit information about groups of aliquots directly in eCAT. All the usual containers are built in to eCAT – freezers, shelves, racks, boxes, and well plates, and eCAT comes preloaded with a wide range of sample templates.
  • To give you a better idea of how easy it is to manage samples in eCAT I am going to play a brief video. Here goes!
  • eCAT is very flexible, and let’s you set up your sample management system to reflect the way your lab works. First, you can create your own containers to be used in eCAT, to house any kind of sample, specimen or even animal. For example, a mouse rack!
  • You can also configure your own sample records. For example, in this plasmid sample template, you can add or delete whatever fields you like. And, you can create your own templates.
  • eCAT fully supports the scanning and printing of cryogenic-safe barcode labels. Everything in eCAT's inventory system has a barcode field, so you can add barcodes to freezers, boxes or samples. Most of the industry standard barcode scanners are supported, so eCAT makes it straightforward to scan in your existing barcodes.
  • So that is brief overview of the inventory side of eCAT. eCAT is also a fully functioning but easy to use electronic lab notebook. You can enter whatever you want into Notebook pages, and format the text as you like. Images, tables, links to web pages, they are all handled by eCAT. You can make links to any kind of data files, and links to other pages in the Notebook or to samples you’ve used in an experiment.
  • Like the Inventory side of eCAT, the Notebook side of eCAT comes with templates for the most common kinds of data, and you can easily create new templates to organize data the way you want.
  • So you have the Inventory side of eCAT and the Notebook side. What’s really special is that the two are linked together. In eCAT the notebook pages and the sample management system are integrated. You can make links from an experiment in the notebook to the aliquots it uses. And groups of aliquots can be linked to notebook information about where they originated. With eCAT, there is no need for two separate systems - you can manage everything in eCAT! And that gives you the benefits we looked at in the first half of the presentation
  • So eCAT is an integrated sample management and notebook application. It’s also a collaborative tool that lets labs and lab members do their research in a friendly and secure environment. You have full control over who can see pages in your notebook. Control is as fine-grained as you like – share a folder or share an individual page. And you can individually specify different kinds of permissions – view, edit, delete and others. You can also send messages in eCAT to co-workers to keep them up to date with your work, and you can attach pages and set priorities on those messages.
  • Access to eCAT requires a username and password, so no one can steal your data. You can establish a signing and authorizing protocol and record those events in eCAT – once a page is signed it can’t be changed, but amendments can be added. There is a full audit trail to support IP protection, and automated backup for your peace of mind. eCAT can be run behind your firewall, or on our secure servers – either way your data is safe.
  • And last but not least, eCAT has been specifically designed to meet the needs of small labs. It’s easy to install and maintain, so you don’t need intensive IT support. And if you have inadequate IT support, Axiope can host eCAT for you. eCAT is fully web based, unlike a lot of offerings which have been build for Windows or MAC with some web features added on. eCATt runs in all browsers, so it is accessible anytime, anywhere. Whether in the lab, at home or at a conference, you can access your data and keep tabs on the lab. eCAT runs on Windows, MAC OS and Linux. So it’s perfect if your lab or institution has a heterogeneous computing environment. As we’ve seen, eCAT is very flexible – to quote an eCAT user, “It’s not tied down to any special area of research. The ability to create templates, and structure your data the way you want to structure it, is a major advantage. Some of the other solutions we looked at had similar functionality, but these solutions are built in a way that you have to modify the way that you work, to work with the solution, whereas eCAT is a solution that will work with the way you are already working, just in electronic format.” And last but definitely not least, eCAT is affordable – pricing is designed to fit the budgets of small labs, not as an afterthought.
  • Thanks for listening. Now I’d like to turn to questions. I’ll start with ones that have already come in, but feel free to ask more as we get into the Q&A.

Managing samples in an electronic lab notebook Managing samples in an electronic lab notebook Presentation Transcript

  • How to manage samples in an electronic lab notebook June 2011 ©Axiope
  • Overview
    • The way we convey information is changing
    • Samples and experiments in labs today
    • Benefits of an integrated approach
    • How it works in practice
    • Q&A
  • Information exchange is changing . . . outside the lab ©Axiope
  • Information exchange is changing . . . Inside the lab ©Axiope
  • But the old ways persist ©Axiope
  • Why integrate? ©Axiope
  • Why integrate? ©Axiope 1. Fewer lost and mislabelled samples
  • Why integrate? ©Axiope 2. Clearer visualization of relationships between samples and experiments
  • Why integrate? ©Axiope 3. Reduction of experimental error
  • Why integrate? ©Axiope 4. More effective search
  • Why integrate? ©Axiope 5. Productivity gains
  • Why integrate? ©Axiope 6. More efficient use of freezers
  • Is integration possible? ©Axiope
  • Yes! Here’s how it works ©Axiope
  • Inventory management system
    • Checkin and checkout
    • Alerts
    • Batch import and edit
    • Freezers, racks, boxes, well plates...
    • Custom containers
    • Sample templates
  • Inventory management system ©Axiope To watch a brief video describing how to manage samples in The eCAT clectronic lab notebook visit the following url
  • Configure containers ©Axiope “ The great thing about eCAT is it’s incredibly flexible in terms of how you can set it up” Prof. Mike Shipston, University of Edinburgh
  • Configure sample records ©Axiope
  • Barcoding ©Axiope
  • Notebook ©Axiope
  • Templates ©Axiope “ I can make templates for different types of experiments, like PCR and flow cytometry” Matt Nicotra, University of Pittsburgh
  • Integrated Solution ©Axiope Experiment Aliquots “ The most important feature is the ability to link records, reagents and experiments, e.g. connect an experimental mouse with the freezer tube containing its tissues” Alex Swarbrick, Garvan Institute Chemical
  • Collaboration
    • Share pages with others or keep private
    • Fine-grained access control
    • Send messages and notifications
    ©Axiope “ With eCAT people can be up to date with what’s happening, make annotations, make changes and suggestions, improving collaboration” Alex Swarbrick, Garvan Institute
  • Protection and Security
    • Secure login
    • Sign and authorize
    • Full audit trail
    • Automated backup
    • Behind your firewall or on our secure servers
    ©Axiope “ It’s backed up, so I don’t have to worry about data disappearing or, even a fire in our lab” Matt Nicotra, University of Pittsburgh
  • Designed for small labs
    • Zero /low IT overhead
      • Easy to install and set up, or
      • Axiope hosts
    • Web based/cross platform
    • Flexible
    • Affordable
    ©Axiope “
  • ©Axiope [email_address]