Tag Archives: lablife

Notes To The Future

Previously I wrote about our move to electronic lab notebooks (ELNs). This post contains the technical details to understand how it works for us. You can even replicate our setup if you want to take the plunge.

Why go electronic?

Lots and lots of lab books and folders.

Many reasons: I wanted to be able to quickly find information in our lab books. I wanted lab members to be able to share information more freely. I wanted to protect against loss of a notebook. I think switching to ELNs is inevitable and not only that I needed to do something about the paper notebooks: my group had amassed 100 in 10 years.

We took the plunge and went electronic. To recap, I decided to use WordPress as a platform for our ELN.

Getting started

We had a Linux box on which I could install WordPress. This involved installing phpMyAdmin and registering a mySQL database and then starting up WordPress. If that sounds complicated, it really isn’t. I simply found a page on the web with step-by-step instructions for my box. You could run this on an old computer or even on a Raspberry Pi, it just has to be on a local network.

Next, I set myself up as admin and then created a user account for each person in the lab. Users can have different privileges. I set all people in the lab to Author. This means they can make, edit and delete posts. Being an Author is better than the other options (Contributor or Editor) which wouldn’t work for users to make entries, e.g. Contributors cannot upload images. Obviously authors being able to delete posts is not acceptable for an ELN, so I removed this capability with a plugin (see below).

I decided that we would all write in the same ELN. This makes searching the contents much easier for me, the PI. The people in the lab were a bit concerned about this because they were each used to having their own lab book. It would be possible to set up a separate ELN for each person but this would be too unwieldy for the PI, so I grouped everyone together. However, it doen’t feel like writing in a communal notebook because each Author of a post is identifiable and so it is possible to look at the ELN of just one user as a “virtual lab book”. To do this easily, you need a plugin (see below).

If we lost the WP installation it would be a disaster, so I setup a backup. This is done locally with a plugin (see below). Additionally, I set up an rsync routine from the box that goes off weekly to our main lab server. Our main lab server uses ZFS and is backed up to a further geographically distinct location. So this is pretty indestructible (if that statement is not tempting fate…). The box has a RAID6 array of disks but in the case of hardware failure plus corruption and complete loss of the array, we would lose one week of entries at most.

Theme

We tried out a few before settling on one that we liked. We might change and tweak this more as we go on.

The one we liked was called gista. It looks really nice, like a github page. It is no longer maintained unfortunately. Many of the other themes we looked at have really big fonts for the posts, which gives a really bloggy look, but is not conducive to a ELN.

Two things needed tweaking for gitsta to be just right: I wanted the author name to be visible directly after the title and I didn’t want comments to show up. This meant editing the content.php file. Finally, the style.css file needs changing to have the word gista-child in the comments, to allow it to get dependencies from gitsta and to show up in your list of themes to select.

The editing is pretty easy, since there are lots of guides online for doing this. If you just want to download our edited version to try it, you can get it from here (I might make some more changes in the future). If you want to use it, just download it, rename the directory as gitsta-child and then place it in WordPress/wp-content/themes/ of your installation – it should be good to go!

Plugins

As you saw above, I installed a few plugins which are essential for full functionality

  • My Private Site – this plugin locks off the site so that only people with a login can access the site. Our ELN is secure – note that this is not a challenge to try to hack us – it sits inside our internal network and as such is not “on the internet”. Nonetheless, anyone with access to the network who could find the IP could potentially read our ELN. This plugin locks off access to everyone not in our lab.
  • Authors Widget – this plugin allows the addition of a little menu to the sidebar (widget) allowing the selection of posts by one author. This allows us to switch between virtual labbooks for each lab member. Users can bookmark their own Author name so that they only see their labbook if they want.
  • Capability Manager Enhanced – you can edit rights of each level of user or create new levels of user. I used this to remove the ability to delete posts.
  • BackWPup – this allows the local backup of all WP content. It’s highly customisable and is recommended.

Other plugins which are non-essential-but-useful

  • WP Statistics – this is a plugin that allows admin to see how many visits etc the ELN has had that day/week etc. This one works on a local installation like ours. Others will not work because they require the site to be on the internet.
  • WP-Markdown – this allows you to write your posts in md. I like writing in md, nobody in my lab uses this function.

Gitsta wants to use gust rather than the native WP dashboard. But gust and md were too complicated for our needs, so I uninstalled gust.

Using the ELN

Lab members/users/authors make “posts” for each lab book entry. This means we have formalised how lab book entries are done. We already had a guide for best practice for labbook entries in our lab manual which translates wonderfully to the ELN. It’s nothing earth-shattering, just that each experiment has a title, aim, methods, results and conclusion (just like we were taught in school!). In a paper notebook this is actually difficult to do because our experiments run for days (sometimes weeks) and many experiments run simultaneously. This means you either have to budget pages in the notebook for each separate experiment, interleave entries (which is not very readable) or write up at the end (which is not best practice). With ELNs you just make one entry for each experiment and update all of them as you go along. Problem solved. Edits are possible and it is possible to see what changes have been made and it is even possible to roll back changes.

Posts are given a title. We have a system in the lab for initials plus numbers for each experiment. This is used for everything associated with that experiment, so the files are easy to find, the films can be located and databases can cross-reference. The ELN also allows us to add categories and tags. So we have wide ranging categories (these are set by admin) and tags which can be more granular. Each post created by an author is identifiable as such, even without the experiment code to the title. So it is possible to filter the view to see posts:

  • by one lab member
  • on Imaging (or whatever topic)
  • by date or in a date range

Of course you can also search the whole ELN, which is the thing I need most of all because it gets difficult to remember who did what and when. Even lab members themselves don’t remember that they did an experiment two or more years previously! So this feature will be very useful in the future.

WordPress allows pictures to be uploaded and links to be added. Inserting images is easy to show examples of how an experiment went. For data that is captured digitally this is a case of uploading the file. For things that are printed out or are a physical thing, i.e. western films or gel doc pictures, we are currently taking a picture and adding these to the post. In theory we can add hard links to data on our server. This is certainly not allowed in many other ELNs for security reasons.

In many ways the ELN is no different to our existing lab books. Our ELN is not on the internet and as such is not accessible from home without VPN to the University. This is analogous to our current set up where the paper lab books have to stay in the lab and are not allowed to be taken home.

Finally, in response to a question on Twitter after the previous ELN post: how do we protect against manipulation? Well previously we followed best practice for paper books. We used hard bound books with numbered pages (ensuring pages couldn’t be removed), Tip-ex was not allowed, edits had to be done in a different colour pen and dated etc. I think the ELN is better in many ways. Posts cannot be deleted, edits are logged and timestamped. User permissions mean I know who has edited what and when. Obviously, as with paper books, if somebody is intent on deception, they can still falsify their own lab records in some way. In my opinion, the way to combat this is regular review of the primary data and also maintaining an environment where people don’t feel like they should deceive.

The post title is taken from “Notes To The Future” by Patti Smith , the version I have is recorded Live in St. Mark’s Church, NYC in 2002 from Land (1975-2002). I thought this was appropriate since a lab note book is essentially notes to your future self. ELNs are also the future of taking notes in the lab.

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The Soft Bulletin: Electronic Lab Notebooks

We finally took the plunge and adopted electronic lab notebook (ELNs) for the lab. This short post describes our choice of software. I will write another post about how it’s going, how I set it up and other technical details.

tl;dr we are using WordPress as our ELN.

First, so you can understand my wishlist of requirements for the perfect ELN.

  1. Easy-to-use. Allow adding pictures and notes easily.
  2. Versioning (ability to check edits and audit changes)
  3. Backup and data security
  4. Ability to export and go elsewhere if required
  5. Free or low cost
  6. Integration with existing lab systems if possible
  7. Open software, future development
  8. Clarity over who owns the software, who owns the data, and where the information is stored
  9. Can be deployed for the entire lab

There are many ELN software solutions available, but actually very few fulfil all of those requirements. So narrowing down the options was quite straightforward in the end. Here is the path I went down.

Evernote

I have used Evernote as my ELN for over a year. I don’t do labwork these days, but I make notes when doing computer programming, data analysis and writing papers. I also use it for personal stuff. I like it a lot, but Evernote is not an ELN solution for a whole lab. First, there is an issue over people using it for work and for personal stuff. How do we archive their lab documents without accessing other data? How do we pay for it? What happens when they leave? These sorts of issues prevent the use of many of the available ELN software packages, for a whole lab. I think many ELN software packages would work well for individuals, but I wanted something to deploy for the whole lab. For example, so that I can easily search and find stuff long after the lab member has left and not have to go into different packages to do this.

OneNote

The next most obvious solution is OneNote from Microsoft. Our University provides free access to this package and so using it would get around any pricing problems. Each lab member could use it with their University identity, separating any problems with work/life. It has some nice features (shared by Evernote) such as photographing documents/whiteboards etc and saving them straight to notes. I know several individuals (not whole labs) using this as their ELN. I’m not a big fan of running Microsoft software on Macs and we are completely Apple native in the lab. Even so, OneNote was a promising solution.

I also looked into several other software packages:

I liked the sound of RSpace, but it wasn’t clear to me who they were, why they wanted to offer a free ELN service and where they would store our data and what they might want to do with it. Last year, the scare that Evernote were going to snoop on users’ data made me realise that when it came to our ELNs – we had to host the data. I didn’t want to trust a company to do this. I also didn’t want to rely on a company to:

  • continue to do what we sign up for, e.g. provide a free software
  • keep updating the software, e.g.  so that macOS updates don’t kill it
  • not sell up to an evil company
  • do something else that I didn’t agree with.

As I saw it, this left one option: self-hosting and not only that, there were only two possibilities.

Use a wiki

This is – in many ways – my preferred solution. Wikis have been going for years and they are widely used. I set one up and made a lab notebook entry. It was great. I could edit it and edits were timestamped. It looked OK (but not amazing). There were possibilities to add tables, links etc. However, I thought that doing the code to make an entry would be a challenge for some people in the lab. I know that wikis are everywhere and that editing them is simple, but I kept thinking of the project student that comes to the lab for a short project. They need to read papers to figure out their project, they have to learn to clone/run gels/image cells/whatever AND then they also have to learn to write in a wiki? Just to keep a log of what they are doing? For just a short stay? I could see this meaning that the ELN gets neglected and things didn’t get documented.

I know other labs are using a wiki as an ELN and they do it successfully. It is possible, but I don’t think it would work for us. I also needed to entice people in the lab to convert them from using paper lab notebooks. This meant something that looked nice.

Use WordPress

This option I did not take seriously at first. A colleague told me two years ago that WordPress would be the best platform for an ELN, and I smiled politely. I write this blog on a wordpress dot com platform, but somehow didn’t consider it as an ELN option. After looking for alternatives that we could self-host, it slowly dawned on me that WordPress (a self-hosted installation) actually meets all of the requirements for an ELN.

  1. It’s easy-to-use. My father, who is in his 70s, edits a website using WordPress as a platform. So any person working in the lab should be able to do it.
  2. Versioning. You can see edits and roll back changes if required. Not as granular as wiki but still good.
  3. Backup and data security. I will cover our exact specification in a future post. Our ELN is internal and can’t be accessed from outside the University. We have backup and it is pretty secure. Obviously, self-hosting means that if we have a technical problem, we have to fix it. Although I could move it to new hardware very quickly.
  4. Ability to export and go elsewhere if required. It is simple to pack up an xml and move to another platform. The ubiquity of WordPress means that this will always be the case.
  5. Free or low cost. WordPress is free and you can have as many users as you like! The hardware has a cost, but we have that hardware anyway.
  6. Integration with existing lab systems if possible. We use naming conventions for people’s lab book entries and experiments. Moving to WordPress makes this more formal. Direct links to the primary data on our lab server are possible (not necessarily true of other ELN software).
  7. Open software, future development. Again WordPress is ubiquitous and so there are options for themes and plugins to help make it a good ELN. We can also do some development if needed. There is a large community, meaning tweaking the installation is easy to do.
  8. Clarity over who owns the software, who owns the data, and where the information is stored. It’s installed on our machines and so we don’t have to worry about this.
  9. It can be deployed for the whole lab. Details in the follow-up post.

It also looks good and has a more up-to-date feel to it than a wiki. A screenshot of an innocuous lab notebook entry is shown to the right. I’ve blurred out some details of our more exciting experiments.

It’s early days. I started by getting the newer people in the lab to convert. Anyone who had only a few months left in the lab was excused from using the new system. I’m happy with the way it looks and how it works. We’ll see how it works out.

The main benefits for me are readability and being able to look at what people are doing. I’m looking forward to being able to search back through the entries, as this can be a serious timesuck with paper lab notebooks.

Edit 2017-04-26T07:28:43Z After posting this yesterday a few other suggestions came through that you might want to consider.

Labfolder, I had actually looked at this and it seems good but at 10 euros per user per month, I thought it was too expensive. I get that good software solutions have a cost and am not against paying for good software. I’d prefer a one-off cost (well, of course I’d prefer free!).

Mary Elting alerted me to Shawn Douglas’s lektor-based ELN. Again this ticks all of the boxes I mentioned above.

Manuel Théry suggested ELab. Again, I hadn’t seen this and it looks like it meets the criteria.

The Soft Bulletin is an occasional series of posts about software choices in research. The name comes from The Flaming Lips LP of the same name.

 

Meeting in the Aisle

Lab meetings: love them or loathe them, they’re an important part of lab-life. There’s many different formats and ways to do a lab meeting. Sometimes it feels like we’ve tried them all! I’m going to describe our current format and then discuss some other things to try.

Our current lab meeting format is:

  • Weekly. For one hour (Wednesdays at 9am)
  • One person each week talks about their progress. It rotates around.
  • At the start, we talk about general lab issues.
  • Then, last week’s data presenter does a 5 minute, one slide Journal club on a paper of their choice.
  • We organise the rota and table any issues using our general lab Trello board.

Currently, we meet in one of the pods in our building. A pod is a sound-proofed booth that seats 8 people on two sofa style seats. It has a table and an additional 2 people can cram in if needed. Previously we used a meeting room, with the presenter stood at the front using PowerPoint with a projector. One week the meeting room was unavailable and so we used a pod instead. It is a lot more informal and the suggestions and discussions flowed as a result. So we have kept the meeting in the pod, using a laptop to present data.

In addition to this, each person in my lab meets with me for 30 min on a Monday morning to go through raw data and troubleshooting. They also present a more formal talk to the centre once every 6-9 months. I mention this to give some context. Our lab meetings are something between “my cloning hasn’t worked” and a polished presentation.

I’m happy with the current arrangement, but we’ve tried many alternatives. Here is a brief list of things you can consider.

 

Two presenters

In my opinion this is a bad idea. We went through a period of doing this so that lab presentations were more frequent, or because we were also doing journal clubs too (I forget which). What happens is that one person has a lot of data and gets lots of discussion and then we either run out of time or the other person feels bad if they don’t have as much stuff to talk about. Accidentally you have made unnecessary competition amongst lab members which is not good. Just go for one presenter. The presenter feels like it is their day to get as much as they can out of the meeting and then next week the focus will move to someone else.

Round-the-table

This is where you go round and people say what they have done since the last meeting. Depending on the size of the group, this probably takes 2 hours or “as long as it takes” which cuts further into the working day. If the meeting is too frequent, lab members can soon get into a groove of saying “nothing worked” each time and it’s difficult to keep track of who is struggling. Not only is it easy for people to hide, the meeting can also become dominated by someone with interesting data. The format also doesn’t develop any presentation/explanation skills. My preference is to keep the focus on one person.

Rotating data talk and journal clubs

It is really common, especially if you have a small group to do data presentation one week and then journal club the next week. My feelings on Journal Clubs are: if they are done properly, they can be really useful and constructive. Too often they regress into the complete trashing of a paper. As fun as this is, it doesn’t teach trainees the right skills. I’d love it if people in the lab were on top of the literature, but forcing people to delve deeply into one paper is not very effective in promoting this behaviour. I think that it’s more important to use the lab meeting time to go through lab data rather than talk about someone else’s work. Some labs have it set up where the presenter can pick data or paper, which means people who are struggling with their project can hide behind presenting papers. I’m not a fan. We currently do a 5-minute journal club to briefly cover a paper and say why they thought it was good. This takes up minimal time and people can read more deeply if they want. I got this tip from another lab. I recently heard of a lab who spend one meeting a month going through one paper per lab member. We might try this in the future. We also have a list on our General lab Trello board for suggesting cool papers that people think others should read.

Banning powerpoint, western films on the table

At some point I got fed up with seeing a full-on talk from lab members each week, with an introduction and summary (and even acknowledgements!). Partly because it was very repetitive, partly because it inhibited discussions and also I felt people were spending too much time preparing their talk. Moving to the pod (see above) kind of solved this naturally. In the past, we did a total back-to-basics: “PowerPoint is now banned bring your lab book and let’s see the raw data”. This was a good shock to the system. However, people started printing out diagrams… these were made in PowerPoint … and before I knew it, PowerPoint was back! Now, there is value in lab members giving a proper talk in lab meeting. Everyone needs to learn to do it and it can quickly get people used to presenting. Not everyone is great at it though and what lab members need from a lab meeting – I believe – is feedback on their project and injection of new ideas. A formal talk from someone struggling to do a good job or overcome with nervousness doesn’t help anyone. I prefer to keep things informal. Lots of interruptions, questions and enthusiasm from the audience.

Joint lab meetings

When my group was starting and I just had two people we joined in with another lab in their lab meetings.   This worked well until my group was too large to make it work well. What was good was that the other PI was more experienced and liked to do a “blood on the floor” style of lab meeting. This is not really my style, but we had a “good cop, bad cop” thing going on which was useful. For a while. If the lab ethos is too different it can cause friction and if the other PI has any bad habits, things can quickly unravel. There’s also issues around collaboration and projects overlapping which can make joint lab meetings difficult. So, this can be useful if you can find the right lab to partner with, but proceed with caution.

Themed lab meetings 

No, not turning up dressed as someone from The Rocky Horror Picture Show… In my lab we work in two different areas. For a few years we segregated the lab meetings by theme. This seemed like a great idea initially, but in the end I changed from this because I worried it set up an artificial divide. People from the other theme started to ask if they could work in the lab instead. There was also different numbers of people working on the two themes. I tried to rotate the presenters fairly, but there was resentment that people presented more often on one theme than the other.  I know some dual-PI labs who do this successfully, but they have far more people. This is not recommended for a regular one PI lab with less than 10 people. Anyway, most labs just work in one area anyway.

Skype and remote lab meetings

For about one year, we had a student join our lab meetings via skype. She was working at another university and it was important for her to be involved in these meetings. It worked OK and she could even present her data when it was her turn. We used the lab dropbox folder for sharing slides, papers and data with her. We still use this folder now for that purpose. I know PIs who skype in to lab meetings when they are away, so that the lab meeting always goes ahead at the same time each week. I have never done this and don’t think it would work for our lab.

Fun stuff – breaking the routine

OK. Depending on your definition of fun… to check on the state of people’s lab books. I ask lab members to bring along their lab books without warning to the lab meeting and then get them to swap with a random person and then ask them to explain what that person did in the lab on a random date. It gets the message across and also brings up issues people are having with recording their data. We also occasionally do fun stuff such as quizzes but tend to do these outside of the lab meeting. I’ve also used the lab meeting to teach people how to do things in a software package or some other demo. This breaks things up a bit and can freshen up the lab meeting routine. Something else to consider to keep it fun: a cookie schedule. We don’t have one, but people randomly bring in some food if they have been away somewhere or they have cooked a delicacy from their home country.

State of the lab address

Once a year, normally in January when no-one wants to do the first lab meeting of the New Year, I do a state of the lab address. I go through the goals and objectives of the lab. Things that I feel are going well, areas where we could have done better. Successes from last year. The aim is to set the scene for the year ahead.

People in the lab can get a bit deep into their project and having some kind of overview is actually really helpful for them (or so they tell me!). Invite them along if you are giving a seminar or use a lab meeting to try out a seminar you are going to give so that they can see the big picture.

Ideas session

It doesn’t happen often that a presenter has nothing to present. The gaps between presenters are long enough to ensure this doesn’t happen. However, sometimes it can be that the person scheduled to talk has just given a bigger talk to the whole centre (and I forgot to check). When this has happened, we have switched to a forward-looking lab meeting to plan out ideas. Again this can break up the routine.

Time

I think 1 hour is enough. Any longer and it can start to drag out. I try to make it every week. Occasionally it gets cancelled when my schedule doesn’t allow it. But if the schedule gets too ad hoc, it sends the wrong message to the lab members.

Wednesday morning works well for us, but we’ve tried Tuesday mornings, Wednesday afternoons etc. I’m happy to set this by the demands from experiments etc. For example, most people in my lab like to image cells Thursday and Friday so those days are off limits. I also ask that everyone comes on time, and try to lead by example. I know a lab where they instigated a 1 Euro fine for lateness, including the PI. This is used as a cookie fund.

No lab meeting at all!

During my PhD we never had a regular lab meeting. Well, I can remember a few occassions where we tried to get it going but it didn’t stick. In my postdoc lab we also similarly failed to do it regularly. I didn’t mind at the time and was happy to spend the time instead working in the lab. However, I can see that many issues in the lab would’ve probably been solved by regular meetings. So I’m pro-lab meeting.

And finally…

Maybe this should have been at the beginning… but what exactly is the point of a lab meeting?

Presenter – Feedback on their project, injection of new ideas, is this the right route to go down? etc. Improve presentation skills, explain their project to others can help understanding.

Other lab people – Update on the presenter’s project, a feeling for what is expected, ideas for their own project. Have your say and learn to ask questions constructively.

PI – Update on project, give feedback, oversee the tone and standard.

Everyone – lab cohesion, a chance to address issues around the lab, catch up on the latest papers and data.

If none of the above suggestions sound good to you, maybe think about what you are trying to get out of your lab meetings and design a format that helps you achieve this.

The post title is taken from Meeting in the Aisle by Radiohead, B-side on the Karma Police single.