Aaron Norman › Comments

I like WordPress blogs, versioned, subscribe to RSS feeds of your student's work, HUGE GPL community. - Dave Lunt

Depends a lot on what you want from it and what kind of work it is supporting. The Southampton systems are getting a lot better and possibly more importantly a lot easier to add functionality onto. For some types of science they are probably good enough - for others, as I guess Mat is finding with wanting to put chemical structures in a native way - its not quite there yet. I find it... more... - Cameron Neylon

Steve Koch's group are the masters with using OpenWetWare, wordpress could probably do a lot of what you want if you've gt people prepared to do a bit of php wrangling...I think the main thing is not to think "I want an ELN" but to think hard about what you want to capture, and how important it is to structure that. A group DropBox folder that people dump Word files into can work just fine if what you want is just a backup and notification mechanism. - Cameron Neylon

I've long wanted somebody to work with Peter Sefton to make ICE into an ELN (http://adlaustralia.org/idea200...) - Bill Hooker

maybe ontowiki (http://ontowiki.net/Project...) - marcin

CAMERON - I want a system where people record EVERYTHING they are doing in their research with links to all data, analyses, output, etc. And I want access to it from anywhere. And I want to be able to search it intelligently. Dropbox won't cut it. - Jonathan Eisen

I built our lab site on drupal, and I have considered adding this sort of functionality into it. Development Seed's custom drupal distribution Openatrium (http://openatrium.com/) looks pretty cool too as an "intranet in a box." I can see that being compatible with your concept. - Walton Jones

@Walton - interesting - Matthew Todd

Jon - OK, that's a big ask to make it work. Technically all this is do-able and it is exactly the concept we are working on. Capture everything, and make connections between things. So what is next on my list is trying to connect DropBox to our blog system. This would mean that dropping any file in gets uploaded - the idea being that a web service is watching the subscribed drop box and... more... - Cameron Neylon

I used WordPress for my undergraduate research project and think it will suite your needs perfectly. There are a plethora of plug-ins available that can add additional functionality, if there is something you need that isn't provided by default and in general it's highly customisable. - Steve Moss

We've been using Wikispaces as the lab notebook and Google Spreadsheets for numerical data for a few years and it meets our requirements. Both have version tracking and we have code that enables full archiving of the notebook and associated raw data files. They are free and hosted so nothing to install and maintain locally. Google Spreadsheets has a nice API for querying and visualization of data if used as a platform to organize data collected from multiple experiments. - Jean-Claude Bradley

@Frank that sounds good. Are there easy ways to link a normal CMS to GIT/SVN? They tend not to be very user friendly, bad interface, which reduces uptake of the whole system in my experience. GIT plugins maybe for WordPress/Plone/Drupal? - Dave Lunt

I don't think there is any Git plugin for Wordpress but if memory serves there are some Wiki frameworks built on a Git backend. I still think worrying about the back end is putting the cart before the horse. Your average lab would probably not benefit from using a versioning system unless they understand what they're for. If they do, then they can probably just use it at the command... more... - Cameron Neylon

An issue tracker such as Trac integrates well with revision control systems, and includes wiki functions. This provides mostly annotation and discussion for the repository, so contributors must still push changes to the code itself. - Mike Chelen

Wordpress is great for logging stuff, but it kinds fails at the intelligent search aspects, unless there's something I'm not aware of - Mr. Gunn

@MrGunn Good point, I agree. Still, it kind of just works as an ELN, and its easy to actually start with today. http://thisiscolab.com/blog... - Dave Lunt

My requirements for an ELN are: (1) Support separate projects. (2) Complete text search. (3) Version manage all content, (4) Everything can be linked and tagged, (6) Display syntax-highlighted code snippets (7) Display images, video, etc (8) Synchronize with my pdf bibliography of references (9) Embeddable intelligent spreadsheets, (10) Display rss feeds and provide an rss feed, (11)... more... - Carl Boettiger

I'm wondering how many people here are experimental (wet-lab) people, and how many are theoretical/computational/electronic people? A lot of the things I'm interested in are to do with capturing the messy process of what happens in an experimental lab so that it can be searched and shared. Is that what everyone else has in mind? - Matthew Todd

My problem is I do both and want one system Sent from my iPad - Jonathan Eisen from email

I've been working on this tool that seems to answer you need: www.symbyoz.com. Give it a try? - Joel

Neil, I think the main distinctions are that in the wetlab things aren't automatically captured in the same way that they all sit on a disk somewhere for computational work. One of the big problems I have is getting people to see the value in making a record of all the samples that they create. There are very few systems that make this easy and natural. And it seems to make no sense... more... - Cameron Neylon

Actually I'd also throw your comment back at you. Descriptions of computational _process_ would be a lot less problematic if computational scientists stopped thinking that just collecting all the outputs was job done and learnt how to keep a high quality wet lab style notebook :-) Versioning systems capture outputs but rarely is there a good record of what _happened_ beyond some sort of commit message or a log file. - Cameron Neylon

I agree with the sentiment but not the details. I think a versioning system is overkill and not really the right paradigm for the lab scientist in most cases. In my experience you generate the data once, and then it doesn't change much. You process it, generating new stuff, but the kind of cycling, tweaking, and branching that VS are built to support doesn't really apply as much. You... more... - Cameron Neylon

There are so many different kinds of data. One researcher might be managing thousands of microscope images every day, while in the same time another could record only a half dozen numerical results. Saving revisions of the images could be pointless if each is only written once and never modified. Whereas putting a document under revision control is a great way to ensure that nothing... more... - Mike Chelen

Ah ok. I think we have a philosophical difference here then. I don't see processing as versioning, for much of my work at least, because it usually generates new objects of new types. I do agree that where you are manipulating a single object in a repeated way, perhaps with branching, then versioning (and branching) is a good way to think about it but I'm less sure that it is a useful... more... - Cameron Neylon

...and I do think that versioning systems (including branch and merge) should be a basic feature of any file system. Just not sure that they need to be surfaced for most users in many use cases. - Cameron Neylon

I'd go further actually, generating, storing, analysing and publishing research objects, explicitly including samples and other physical objects. And I think the "computational thinking" approach might be even better applied to the physical world. - Cameron Neylon

Cameron I think that the requirements for version tracking may differ between labs. In my lab we often have lots of undergrads recording their lab notebooks and it would be unusual if there was no error correction for an experiment at some point. It is also not uncommon that the Google Spreadsheets we use to record the raw data and show the mathematical processing often initially... more... - Jean-Claude Bradley

If you want everything consistently done in git the documentation part could be handled with toto - "a git-powered, minimalist blog engine" (http://www.cloudhead.io/toto) (not sure if you need commenting functionality) - Konrad Förstner

We've been very happy with http://www.unfuddle.com Unfuddle. It includes notebooks, though I don't know how appropriate these would be for experimental data. The integration of the subversion repository with tickets / milestones / projects is very nice. - Ruchira S. Datta

biological data, at the point of capture, is really messy, and you often have to iterate several fast optimization kinds of assays or experiments before you hit on the set of conditions under which you can capture clean or meaningful data. Then once you do get close to clean, it's off to the next set of optimizations for the next thing. That's the dynamic that computational tools fail... more... - Mr. Gunn

A bit late to the party (via Cameron's post on the Daily Scan), but back in February I was sat in a dull seminar and made these notes. A Data Analysis Deposition System e.g. to store all the R code used to turn data X + Y into results Z. - load source code for analysis pipeline - check data dependencies, on submission and periodically in future (e-mail owner if links go down.) -... more... - Dave

Open Source www.Bikalabs.org develops web and CMS based LIMS - used in chemistry, agriculture, water quality, environment and inter-laboratory sectors. A public health lab branch is currently in development. Your requirements are research orientated, batching per project and full text admin are gaps in Bika that can be plugged. Full Plone CMS functionality is available. Analysis work... more... - lemoene

I've been using git for curating my (text based) data analysis in the social sciences, and I've been impressed with its usefulness for keeping a very detailed history of what I've been doing. The only problem is for large binary objects, but apparently that's being addressed. Gitalist: http://search.cpan.org/perldoc... is a front end to git which can be easily modified to provide... more... - k d

There has been some very interesting discussions here, and a lot of questions that are commonly asked. There appears to be a lot of discussion about using software that has not been specifically designed to be an ELN and some people find that these are perfect for what they need them to do. However, it is important to outline your requirements (as has been done above). I work for... more... - Aaron Norman

I'm developing a collaboration tool for researchers called SciTecMed [ http://www.scitecmed.com ]. It is like a mashup of dropbox and github. I'd appreciate an opportunity to show the demo and learn more about your needs. - SciTecMed

hey scitecmed - drop me a line - am interested in this jonathan.eisen@gmail.com - Jonathan Eisen