Tag Archives: organisation

Adventures in Code V: making a map of Igor functions

I’ve generated a lot of code for IgorPro. Keeping track of it all has got easier since I started using GitHub – even so – I have found myself writing something only to discover that I had previously written the same thing. I was thinking that it would be good to make a list of all functions that I’ve written to locate long lost functions.

This question was brought up on the Igor mailing list a while back and there are several solutions – especially if you want to look at dependencies. However, this two liner works to generate a file called funcfile.txt which contains a list of functions and the ipf file that they are appear in.

grep "^[ \t]*Function" *.ipf | grep -oE '[ \t]+[A-Za-z_0-9]+\(' | tr -d " " | tr -d "(" > output
for i in `cat output`; do grep -ie "$i" *.ipf | grep -w "Function" >> funcfile.txt ; done

Thanks to Thomas Braun on the mailing list for the idea. I have converted it to work on grep (BSD grep) 2.5.1-FreeBSD which runs on macOS. Use the terminal, cd to the directory containing your ipf files and run it. Enjoy!

EDIT: I did a bit more work on this idea and it has now expanded to its own repo. Briefly, funcfile.txt is converted to tsv and then parsed – using Igor – to json. This can be displayed using some d3.js magic.


Part of a series with code snippets and tips.

Advertisements

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.

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.