Sep 052014
 

I received an email from Alex Lang and he asked about my current use of Electronic Lab Notebooks

Hi Dave,

I’m a physics graduate student who just started using a WordPress based ELN. I really found your thoughts on ELNs helpful, especially:
http://www.davelunt.net/evophylo/2009/03/wordpress-as-eln/
https://speakerdeck.com/davelunt/electronic-lab-notebooks-for-ug-students

Since someday I want to be a PI, I had some questions for you. If you would prefer to answer as a blog post, that would be fine by me.

I wondering if you could elaborate more on the mechanics of how you actually implement ELNs with your students. For example, some questions I had are:

Do students have an ELN on your website? Or do they host their own?
What happens when students leave the group? How do you keep a record of the ELN?
Does the whole lab share ELNs with each other? Or do you restrict it to you seeing students ELNs?
Do you ever share parts of the ELN with collaborators / outside people? Does that work out?

Thanks again for the insight into ELNs!

Alex

Hi Alex, thanks for the prompt to write something

Even though it was quite a while ago that I wrote my posts about ELNs most of it still holds for me. The post you link to above was talking about graduate students and postdocs, whereas the slides refer to undergraduates doing a short project but actually both are implemented in a similar way.

Do students have an ELN on your website? Or do they host their own?
What happens when students leave the group? How do you keep a record of the ELN?

I can answer these two together. I set up a blog ELN for all, and nobody sets up their own. Two reasons for this: Firstly, setting up a blog can be intimidating if you’ve never done it before, as many starting an ELN have not. Secondly, the blog is owned by me and can’t easily be deleted. This ensures I always have the experimental record even if researchers leave. I think this is important. Of course the researcher has admin rights and can always save a copy when they leave and take it with them, but I always retain the ELN record.

I host all ELNs on WordPress.com. The reason is that I trust them more than I trust my personal domain. You will have a reduced list of themes and plugins that can be used, but it is fast and robust.

Does the whole lab share ELNs with each other? Or do you restrict it to you seeing students ELNs?

Actually, only the project supervisor (me) usually sees the ELN. This is not really a decision, just how it worked out. I would be happy to let anyone in the lab see, and the people writing the ELN probably wouldn’t mind either, but nobody really wants to read the experimental minutiae apparently. We have regular lab meetings and this provides all the details most people want. Sometimes I will add a postdoc and a PhD student onto each other’s ELN if they are on similar projects, but generally people are happy without seeing details. In some ways I think this is a shame, we can all learn something from seeing how others do science and write up the record. I may try to change that and put everyone on every ELN by default.

Do you ever share parts of the ELN with collaborators / outside people? Does that work out?

I have shared an ELN with another co-I on a grant. It worked well, though it was not a major source of info for them (I don’t really know how often they read it). They preferred meetings where the researcher would summarise and discuss rather than reading the experimental record (which is sometimes a bit dry). Other co-Is have not really wanted to even see the ELN. I however quite enjoy enjoy browsing new work by my people and I am excited when I get a new post notification!

This brings me to something I hadn’t really thought much about before. Use of ELNs is not primarily a technology issue, it is a personality issue. If you don’t want to read a paper notebook, you won’t want to read an electronic one. Even if you don’t want to read other ELNs you should still keep one yourself:

  • It will help you in writing your manuscript. Some descriptions and methods will already have been written and only require copy/paste. I recently saw an excellent ELN post by my postdoc Amir that was a manuscript draft. Just explaining in the ELN what had been done and what conclusions could be drawn had created that first manuscript version.
  • It is more robust. Your leaking ice bucket cannot ruin the whole year’s experimental record. There is version control. It is backed up in the cloud and if you are wise it has a regularly saved local copy too.
  • The features of a WordPress ELN make it powerful. Search, tags, and categories make my day much easier and more productive.
  • I think it is just easier to keep information this way; easier to paste in text, and screenshots, and protocols, and web links. Even for people working at the bench rather than the computer I think it is easier.

My personal ELN is still very successful I think. I don’t research every day which makes the search function vital. I have had some minor failures but it is the best experimental record I have ever kept. My failures have taught me about the value of records with lots of searchable tags, the importance of explicit data file versions, and never to scribble something to ‘type up later’. The times the ELN gets flaky is when I’m too impatient and do the next thing before really creating a record for the last.

I have 2 students starting later this month, and I will set up a WordPress blog ELN for each. If anyone would like to add their views and experiences please leave comments, or email me.

 

Nov 122011
 

I’ve been trying out the KCite plugin for WordPress. This has been created to make WP a better scientific publishing platform- and so far I’m really impressed. Install the plugin in the usual way, there’s nothing really to set up, just start using it. To add a reference(10.1093/gbe/evr090) you have to include a shortcode in the blog post with the doi. I can’t show that here directly as it will automatically be formatted when the post is published so I’ve included a screenshot. It is also possible to use the PubMed ID(18606000) instead of doi, which is an option in the settings panel or else you can specify source=’pubmed’ in the opening citation tag as I did with ref 2 (although you can’t see that).

KCite shortcode to insert a reference

One nice aspect is that the plugin formats a bibliography at the end of your blog post. I’ve had no problems with the plugin at all. Of course it is early days and it isn’t a fully-featured reference manager like desktop workhorses Zotero or Mendeley, but it is already very useful.

One slight problem I have is that several of my publications are in areas of biology not covered by PubMed, and I have two with broken doi numbers, one because it directs to somebody else’s paper (its fixed!) and one because Nature can’t spell and I refuse to link to a mangled website version of my paper.

What additions would I like? Not much really. I would like the ability to have reference summary popup on mouse-over the reference, that would be a useful thing for a web-based citation. Also perhaps more web-links from the reference section? I could name lots of other things but that wish list would be turning it into a fully-featured reference manager, which is unrealistic for a recent effort by academics rather than some large company. To be perfectly honest I’m surprised that there aren’t WordPress plugins already for Mendeley and Zotero.

The plugin was created by Biologists Phillip Lord, Simon Cockell, and Daniel Swan, who together run Knowledgeblog. The following quote describes their mission.

Welcome to Knowledge Blog. We are investigating a new, light-weight way of publishing scientific, academic and technical knowledge on the web.

The Problem

Scientific and academic publishing is a painful process for authors, reviewers and readers alike. No one really benefits from the current system which grew because of the expense of producing, printing and distributing books. The internet and the web technologies have changed this enormously, but still the uptake within scientific and academic publishing has been slow, and left much of the existing system in place; the reason for this is that some parts of the system are good: explicit authorship, peer-review and the ability to archive are the main ones.

We need a new solution, that removes the annoyances of the current system, while keeping the advantages.

The Solution

The solution is already available; we just need to use it in a different way. Blogs and blog technology has been designed to allow people to discuss, share and disseminate their opinion in a simple and light-weight way. Adding a little formality to this, and we have a journal.

Very interesting indeed, something I’m going to keep a close eye on. As for KCite, I can see it being regular addition to my posts.

Bibliography

Mar 072009
 

In my previous post I said that I needed to find out about associating data files with electronic lab book entries. I think I’ve got it sorted out now. Imagine you are recording an experiment and want to associate the actual data files with the post of your ELN blog. I don’t mean put the actual text there, rather a link to the file of whatever format.

In the post toolbar Upload/Insert area click on the last icon “Add Media”. You should then be in the “Add files from your computer” area. This doesn’t work for me and I have to click on the link that says “browser uploader” instead. Select the file from your computer and upload it. When it has uploaded you will see the details screen. Give the file an informative name as this will be the link text inserted into your blog post by default. If nothing much happens when you click “insert” then make sure you have clicked on the “File URL” button. This will add a link to download the file into your post. The actual files themselves are held in

domainname/wp-content/uploads (then year and month folders).

These data files are not backed up if you ‘export posts as xml’ as your backup strategy, but its easy enough to ftp a copy weekly, or even get a script to do it.

I normally fill my ELN with methods and conclusions and things to do next. I keep the data files and results archived locally and try to include the file name and location in the notebook (if I remember). Now I’ll move to keep both together in WordPress. It feels a much better arrangement, and I hope I will spend less time looking for the exact input file that generated a specific tree.

Mar 032009
 

In my previous post I said that I had been testing software and decided that the new version of WordPress would be my electronic laboratory notebook (ELN). This post details some of the reasons.

WordPress is open software under a GPL license, allowing it to be distributed and modified. I really like this. There is a very large and active community of people supporting it. This means that even if WordPress HQ was hit by a meteorite tomorrow the software would be unlikely to die. Like Evernote (that I mentioned previously) WordPress exports as xml, but in a standard format that can be easily imported into Blogger or other software. It can also be made to export posts as PDF and MSWord via plugins. I can’t think of anything more important than having my data in easily interchangeable formats, I have changed my mind about ELNs before and I don’t want to be locked in.

Syncing: Since blogs are ‘on the web’ they are accessible from anywhere and cannot be out of sync.
Style: WordPress2.7 is very slick and attractive software indeed. More importantly since content and style are separate entities you can swap between >600 free themes. Yes, I know it still sounds superficial to be so worried about how it looks, but you will have to live with your ELN for years! I need flexibility to control appearance and layout. Beyond appearance WordPress2.7 has a lot of flexibility to control different aspects of your environment.

Other aspects of WordPress
Plugins: There are over 4000 community developed plugins to extend functionality. If its not there you could write it yourself. These include several functions I’ve become interested in using:- exporting posts as PDFs for archiving the last few months activity, automatically colouring code snippets, posting from pre-prepared templates.
Comments: I’m thinking primarily about my own use at the moment, but would like to use this with students and postdocs too. Sharing and commenting is very valuable.
Versioning: WordPress2.7 has a good, wiki-like versioning system. This is useful if you update an experiment and need to see exactly what changes you, or a lab-member, has made. Here are a couple of screenshots.

Privacy: This system allows you to implement your own level of privacy, from completely open, to selected users, to complete privacy according to your preference. I have thought about this issue quite a bit and implemented a private ELN for myself. If you come to different conclusions it is possible to allow selected users to subscribe, edit, author or administer as required.
Tags and Categories: The combination of categories (“selection”), subcategories (“hemagglutinin”) and tags (“dN/dS”) works better for me than just tags or just hierarchical folders.
“Press This”: the (strangely named) javascript button can be dragged into your browser and can be used to add selected text or the page as a blog post whenever you come across something. It isn’t as good as Evernote’s capture tool, but it captures text fine.
On the move: There is a WordPress application for iPhone/iTouch and other mobile devices. Posts can be emailed in too.

Something I’m not sure about yet is associating (non image) data. If I have an excel spreadsheet that is part of an experiment I believe I can upload it and then link to it from within the blog text. If I’m right that would be useful as it would permanently keep data and description together. The data files would then just be in an ftp-accessible folder on the server which I suppose could be backed up with a script. I’ll have to investigate more and see if this really is the case.

I tried WordPress out with a free blog hosted at wordpress.org. I used this for a while, but wasn’t entirely happy with the flexibility. The themes I wanted weren’t among those available and it isn’t possible to install plugins there. So although it was quite functional I decided to rent my own domain hosted at DreamHost. That is what I’m working with now, and in a post soon I’ll sum up my experiences both good and bad. Overall I’m quite happy with it though.

Mar 032009
 

Last year I posted about my search for an electronic laboratory notebook (eln). Since then I’ve had experience of several systems, and my ideas have changed quite a bit, so I thought it was time for another post.

I listed a number of criteria that I thought were important for my eln. I got it wrong however, it turned out that two of the things I valued most weren’t even on my list- synchronization and style.

Synchronization
I was at that time using journaling software, and syncing using either their internal capabilities to link to my .mac account, or later on using the excellent Dropbox to sync. This worked well 99% of the time, but 99% isn’t enough. I wanted my eln to be in perfect sync between work and home and NEVER get corrupted by conflicting changes. So I abandoned these journaling software elns despite the nice software.

Style
This sounds superficial, but I realized that using attractive software is very important to me. I spend most of the day working with my lab book, and I just can’t commit to using something spartan and ugly. I want to use a modern software environment that is attractive and well laid out. I was initially put off blogs and wikis not just because they are generally short of features but because most are really ugly to work with.

(Its not all about sync and style, I want many other things too, but I’ll discuss those specifically in a follow-up posting)

I’m impressed with Evernote, and seriously considered this as my eln. It works very well in fact, yet I have decided not to go this route. Evernote is proprietary software, which isn’t a deal breaker for me, but compared to many it has very poor export. It will export your data as an xml file, but as far as I can determine this xml file cannot be opened by any other application. If Evernote went out of business tomorrow could I get at my information? Well, the local copy would still work with the application but I would not be in a good situation at all.

So, having researched this quite a lot, I have decided that my eln will be WordPress. Not any blog, but specifically the new WordPress 2.7. I’ve been using it for 2-3 months now and I’m going to write why I’ve chosen it, and how I’m using it, in a following post.

Blogs have been discussed and used for eln before. I’m not suggesting a whole new approach here, just recording my personal experiences in finding an eln solution that works for me.