Interview with Nick Oswald of Bitesize Bio, the Online magazine and community for molecular and cell biology researchers

Posted by Rory on November 3rd, 2010 @ 10:40 am

Something a bit different this week, a post not directly related to electronic lab notebooks.  But it should still be useful for those with an interest in ELNs.  I‘m going to introduce our Edinburgh-based neighbor, Bitesize Bio.  Bitesize Bio provides ‘Brain Food for biologists’.  Free brain food, I should add.  Bitesize Bio is packed with practical information for biologists working in labs: information about tools, software, techniques, life in the lab, your career, you name it and it’s likely to be found on Bitesize Bio.  I thought the best way to provide an overview of Bitesize Bio is to let its founder, Nick Oswald, describe it.  Here’s what Nick had to say.

Rory:  Give us a top level view of what Bitesize Bio is all about.

Nick:  Bitesize Bio aims to bring together all of the technical and vocational know-how that molecular and cell biology researchers accumulate through years of experience into a central place where it can inspire and educate other researchers. But Bitesize Bio is not just a series of written articles – the community that has developed around the website adds another dimension by adding their tips, questions and viewpoints to individual articles and also seeking and giving assistance to each other in our new Questions section. I think that the combination of considered, insightful articles and lively input from the community is what makes Bitesize Bio such a useful and interesting resource.

Rory:  The site has developed into a great resource for biologists.  How did you get started?

Nick: I was working as a molecular biologist for a small biotech company back in 2007 and was looking for a change of direction. Since training/educating people was the part of the job I enjoyed most, I started writing down the training and tips that I was giving people in the lab, then began publishing it in a blog. Once it started to attract attention, people came to me asking if they could write something for us and it just snowballed from there.

Rory:  Tell us a bit about the community – what kinds of people visit Bitesize Bio?

Nick: The site was originally intended for PhD students, but we have been pleasantly surprised to find that researchers across the full spectrum of experience regularly use Bitesize Bio. As I mentioned, the community aspect of Bitesize Bio is vitally important so the input of the more experienced users really enriches the site.

Rory:  One of the things I like about Bitesize Bio is that you are always introducing new features.   What’s in the pipeline at the moment?

Nick: Well, earlier this year we piloted a series of six webinars on various topics related to PCR. They proved a real hit so now we are looking to put together a full webinar program for 2011 where each week we will present a live webinar on a technical or vocational topic of interest to our audience. We are excited about the prospect of bringing really useful lectures into labs all over the world throughout 2011.

Rory:  I know you are always looking to get new people and organizations involved with Bitesize Bio.  If someone has an idea or a suggestion, what should they do?

Nick: That’s right Rory, we are always open to new ideas from individuals, institutions or companies for new additions to Bitesize Bio. We also gladly accept contributions of articles, videos or webinar topic suggestions. If anyone would like to  get in contact about any of this (or just to chat in general about the site) they can email me on nick [at] bitesizebio [dot] com.

So there it is, Bitesize Bio.  It’s already a great resource for biologists, and it’s always developing.  Definately worth a look at www.bitesizebio.com.

What is an electronic lab notebook?

Posted by Rory on July 6th, 2010 @ 9:30 pm

Welcome to the electronic lab notebook blog.  This will be a space for discussing electronic lab notebooks from every angle:  what benefits do they bring? how do they compare with alternatives? what kinds of features do they have and should they have? what issues do people face in using them?  how can you get the most out of them?

In this first post I’m going to start at the beginning:  what is an electronic lab notebook?

Wikipedia defines electronic lab notebook as “a software program designed to replace paper lab notebooks“.  That could be just about anything — beauty is in the eyes of the beholder!   I’ll take a look in a second at who the relevant beholders are and what each of them thinks, but taking wikipedia as the starting point it’s  fair to say first that all of them are looking to move away from this:

Postdocs and graduate students

So who are the relevant beholders?  They can be divided into two categories.  The first is people looking for an electronic note taking device for themselves.  They tend to be interested in convenience and simplicity.  Something which is easy to use and also helps them get organized.     But many postdocs and grad students want something which also provides  support for research.  Here is one description of the ‘dream app’ over on an Apple forum about electronic lab notebooks:

  • easy copy-pasting/drag ‘n drop
  • ability to re-open the files
  • metadata and search (tags, keywords, …)
  • possiblity to link to older notes and graphs
  • store PDF (or TIFF) representation of external files along with the original file: preview files without their originating application
  • automated backup mechanism
  • encryption on disk

The thread following that post contains a good discussion of the varieties of things people want in an electronic lab notebook for their own use, examples of what they have tried, what they like and dislike, and the limitations of the available tools.

PIs

The second category of people looking for an electronic lab notebook want a collaborative tool rather than one aimed at individuals.  They tend to be PIs, or in some cases others in the lab who’ve been asked by the PI to identify a suitable tool. Like those looking for an individual tool, PIs want something which is simple to use and easy to learn.  But beyond that their needs diverge from that of individual scientists. Professor Mike Shipston of the University of Edinburgh provides a good summary of the kinds of challenges that drive PIs to look at adopting an electronic lab notebook:

“We generate a wide variety of types of data sets, for example data from molecular analysis, quantitative analysis, for example quantitative RTPCR, gene cloning, through to electrophysiological analysis, for example from confocal images and total internal reflective microscopy right up to behaviorial assays in animals.  So its really about coordinating those types of data sets that fit together, keeping them contained within projects, because the data sets are derived from different people within the lab.  Also we have a very big extended network both in the UK and across Europe and the US.  It’s about keeping that information together. We have a large number of people coming in and out of the lab, the challenge is keeping track of that data and integrating it in with data from existing projects.”

Well that’s it for this first post — I realize I haven’t yet provided an answer to the question of what an electronic lab notebook is!  The next post is going to look at the tool that has been most widely adopted by labs looking for a collaborative tool, wikis.  I’ll discuss the strengths and limitations of wikis and whether they do – or should – qualify as electronic lab notebooks.  And don’t worry, I promise to come back with a specific answer to the question of what an electronic lab notebook is.