Posted by jrdixey on February 20, 2010 at 2:46am
As this group has grown - 38 members last time I looked! - I thought it might be time to find out what everyone is up to. How are you using - or planning to use - Drupal in science? If you're running part of your lab with Drupal, how does it fit in with the rest of your systems? Are you using it to collaborate with other labs or institutions?
Comments
a sample submissions/booking/logging system
Hi JR,
since you ask ...
the small molecule X-ray crystallography lab I work in was looking for some method to capture all the metadata associated with an actual experiment - along with some kind of booking/scheduling/logging system for the instruments. Currently we have a "paper" based office. On and off (but mostly off) I was trying to write a (in principle open source), largely self-contained, Drupal-6 module to do this. Our lab offers a structural analysis service, as well as student training and use. So we have internal/departmental users, internal and external clients, and a very small number of dedicated staff. We aren't high-throughput, don't need any kind of sample tracking, so full blown LIMS is a bit of an overkill, as I understand it.
I tried to document things a bit, but its not so advanced (nowhere near the scope/power/quality of what Rudy van der Blom has shown!), and since I started there's been a push for a departmental wide booking system for all analysis services (not just our lab), so my attempts will likely be abandoned in the near future anyway.
But apart from all the great table presentation features, Drupal allowed us to authenticate internal users to a departmental mail server, still using Drupal's authentication for external client accounts, so that fitted our requirements quite well. Thats about as integrated as its likely to get.
cheers
d
Hi doobs, Great to hear that
Hi doobs,
Great to hear that you are thinking of using Drupal as an internal tracking / data system for your experiments and samples. Although, the DIF system I've shown does perhaps sound a bit complicated or huge, the truth is, it isn't, and that is the power of Drupal.
A system like you described could be developed in a couple days. Apart from the DIF system, I've made some "disposable" systems which are/have been used for just one project (= a couple months) and after that I've just deleted them again after they had served their purpose.
Hi Rudy, A system like you
Hi Rudy,
Ohhh, don't say that! I spent a month and a half on it already ;)
(Note to self: Learn to code like the wind, and don't sleep!)
Maybe I was trying to do things the wrong way, building (i.e. with hook_schema, db_query etc.) and formatting (forms API) my own tables?
(clutching at straws)
d.
My first approach
Hi d,
Usually I don't start writing my own modules right away. First I pencil draw what I want the system to do, then I'm searching for modules or combination of modules which could do the trick, and if it is necessary then I start to code myself. Use the power of drupal, since in the most cases there is already a module in more or less the form you want it to be, just tweak it to your needs.
Rudy
LIMS for biological samples
Hej Rudy,
i was screening the net for solutions for building a LIMS for tracking lab samples, experiments etc. and the only page i found was your commentary ;).
Before i try to build it from scratch with CCK, Views etc., i like to ask you, if you can recommend any modules or if you have a link to an open source system like that?
I found http://www.open-lims.org/ but its not based on drupal...
Thanks,
Greetings,
Rudi ;)
Drupal modules LIMS
Hi Rudi,
My most used modules for building management systems with drupal are:
views_customfield
Automatic nodetitles to create subsequent project numbers
Greetings,
Rudy
Interesting!
Hi, very interesting writeup. I read your documentation with interest. Thanks for putting it out there.
Jennifer
Hi, Jennifer! I'm building
Hi, Jennifer!
I'm building some kind of database for detecting and watching for those child who falled ill with neuro-oncology.
We have very badly state of this things here in Russia. There’s no statistical information about these children. They coming to Moscow there they have an operation, then the radiotherapy and then the chemotherapy etc. And all of this treatments in different clinics and institutes. So we decided to create some database where we can store some information about these child and they cure for Moscow clinical institutes. I want to use cck, views and rules for this problem. CCK helps to define some mainly objects (content types) like child, surgery, chemotherapy, radiotherapy, clinics and users (doctors). When using node references we can link them and create many tables as we want using views. Also we can collect some statical information using custom querys by views filters, we can builds some statical presets. And we can create chronologies using revisions system with some rules. This’s very strongly and effective mechanism. I created large and strongly database for Grant Life foundation using this mechanism (which is one of the largest foundation in Russia, they helping childs who falled ill with leukemia and some kind of neuro-oncology illnesses). Lets look at mainly parts of this database – it’s very-very-very strongly system which collect statical information for all clinics, doctors, volunteers and diagnosis with which we work. I make few screenshots for you.
http://img687.imageshack.us/img687/2458/controlpanel.jpg
http://img294.imageshack.us/img294/849/childrencopy.jpg
http://img121.imageshack.us/img121/2266/childpage.jpg
Main page is draggable and droppable control panel which show different information for different users and different roles. We have even volunteers in this database which can see only some part of information about young patients from clinic where they works.
Next screen from main part of base where you can find any child with many useful filters. I just translated primary menu for you. And then in the third screen you can see child page. Actually we have these pages for all doctors, clinics and many-many others where we can see some statistics which our base’s collecting every day. Unfotently I can’t tell you how it’s working and what it can do, because I usually spend many hours on this story.
In the meantime, I thought - what's the difference between statistical
problems from different sciences? And I think this difference is in
information (fields) and mathematical methods which can implement by
special programs like wolfram's Mathematica.
So, I want to create some kind of framework tool for statical science in drupal which can collect easy definded information to database, make a similar analysis and export it from this tool in some format like xml, csv, xls or another.
I think it’s possible, look at development seed’s works and how they analysis data.
My Drupal for Science
Hi.
I have built a D5 website, ZERCULATOR Expert Systems, to provide users around the world with free scientific calculation tools that would normally be tedious or complex when done manually.
Currently, it supports tools in probability and statistics. In subsequent releases, it will diversify into physics, mechanics, operations research, and various fields in engineering.
Regards,
Rez
I recommend for Email Newsletters & Email Marketing - YMLP.com
Pretty cool
That's pretty cool. Out of curiosity, what are you using on your backend for the calculations? Are you using PHP code or are you using a service with another package? I have thought of doing something like this using rApache, but have yet to implement it.
Yes PHP
Thank you sir.
Yes, the calculations are done in PHP and incorporated into Drupal modules. No external packages needed.
PHP is quite formidable. Later on, I will experiment with it for matrix calculations.
Regards,
Rez
I recommend for Email Newsletters & Email Marketing - YMLP.com
Moved to a new domain name
My project is now is now at http://zerculator.tk
I recommend for Email Newsletters & Email Marketing - YMLP.com
I'm building Sensor Hub, a
I'm building Sensor Hub, a suite of modules to aid in collecting and analyzing sensor data. http://drupal.org/project/sensor_hub