Upcoming changes and improvements in 2012
23rd December 2011 11:39 by Roman Konertz (comments: 0)
A letter to our Users
Dear (potential) Open-LIMS user,
On 23rd December 2010, the first public version of Open-LIMS was published. A lot of things has improved during this year. I will give you a small introduction in our upcoming changes and improvements for next year.
Waiting Screens and Dialogs
After reading a study on intdesign2011.blogspot.com, we will try to avoid waiting screens. In most parts of Open-LIMS, the user will see a waiting screen for a period of 3 seconds (see Fig. 1).
In the current public version in 'Create Project', 'Create Sample', 'Clone Sample', 'Login' (Fig. 2) and 'Logout' a new waiting screen is implemented.
In addition, several features will be moved in a dialog window. For Example: Project Proceed (Fig. 3), Add File, Add Equipment and Add Value. Besides, every “yes/no”-dialog, (“delete” or “cancel”) will be moved in a dialog without waiting-screens (e.g. “delete project” (Fig. 4) or “cancel project” (Fig. 5))
The waiting screens will be removed from most frequently used functions first.
Moreover we want to change the lists, to avoid permanent reloads. The first phase is the implementation of an AJAX list handler. This handler is still implemented at the most lists (Fig. 6; except Search and Administration). The second phase will be the functionality of resizeable and concealable columns. In parallel to dialogs, we will start from most frequently used functions to less important ones and finish with the administration.
A special list is the Data-Browser. A lot of operations are possible in this list, e.g.:
- make all important operations in the data-browser in a menu (Fig. 7)
- delete multiple items in one action (Fig. 8)
- adding Files, Values or Folders (Fig. 8)
- direct download from the Data-Browser (Fig. 10) and not via the “File-Detail” page
As we described in this article, we want to enable the user to enter material related data. The differences between: material, samples and projects are shown in figure 11.
While entering value-data into forms, some users need to compare these data. Generation of charts would be a nice function. We will implement the comparison of two or more values and of two or more samples. Possible chart-types would be a bar-chart, a pie-chart, a line-chart and a scatter-plot.
DIN EN ISO/IEC 17025 Conformity/Client-Management
The last part is the implementation of the requirements of the DIN EN ISO/IEC 17025. The main missing parts are the client-management and the management of laboratory documents. The implementation of the conformity is one of our minor tasks, but with a client-management we will enable medical or material-science laboratories to use Open-LIMS.
On the way to our first stable version (Version 0.4.0.0), we will try to publish a snapshot of our current development status, every 6-10 weeks, called “Version 0.3.9.9-X”. If all features and bug-fixes are implemented, we will switch over to 0.4.0.0. An update from version 0.3.9.9-X to 0.4.0.0 will be possible.
I have read an article on limsexpert.com which criticizes that Open-LIMS has no installer (and some other things as well). We will not create an installer at the moment. Open-LIMS needs a PHP-Environment with special extensions (e.g. 'imagick' for handling tif-files) and cannot be installed in a WAMP/LAMP/XAMPP environment. In detail: Open-LIMS needs PostgreSQL and Imagick which is not available in these environments. The installation-administrator needs some IT knowledge. In my opinion, we can expect, that this person can import a database via the command-line and modify a configuration file. Depends on demands, we will publish a version which runs in a WAMP/LAMP/XAMPP + PostgreSQL environment (without the support of tif-files of course) later, but this is a less than minor task.
Finally, we have created a Skype-Account (“open-lims”) for irregular instant-message and voice communication.
We hope, that Open-LIMS is useful for you and wish you a happy new year.
Creating an Upload function with a progress meter
19th October 2011 15:48 by Roman Quiring (comments: 0)
Uploading custom files to the database is an integral part of Open-LIMS. However, due to technical restrictions, for a long time it was not possible to display any information regarding the progress of an upload. This can be very annoying for the user, especially if he wants to upload a lot of files at the same time: He is doomed to wait for all files to arrive on the server without knowing when this will happen or how many files have already been transferred. The reason is simple: PHP is not capable of tracking uploads. It just copies the files from the POST-header and returns a status message when it’s done, so there is no way of knowing how much of a file has been copied until the upload is finished.
Now you might say “but hey, I could just check the size of the partly-copied file on the server”. Yes, you can, but it’s a hard job. PHP stores the file in a temporary folder (which you cannot access from within PHP itself) with a random temporary filename (which makes it difficult to find the current file), so the only solution for this is an external Java or Perl script.
Fortunately, some smart people came up with an easier solution: A small PHP extension called uploadprogress (http://pecl.php.net/package/uploadprogress). All you have to do is to add a hidden input field with a unique ID at the very beginning of your upload form, so the extension can keep track of it:
Material Management Module
24th August 2011 14:34 by Webmaster (comments: 0)
Today, Open-LIMS manages data in two modules, "project" and "sample". After a long period of reflection, we think that Open-LIMS needs a third module which saves laboratory-data. The new module should manage lab-material. Based on our experience during our internal tests, it is not possible to save that data at the moment. Material should be organisms, chemicals or other substances. It should be divided in a generic information part – a catalogue of components – and concrete information part which saves the material data.
To comprehend the differences between the modules and the generic and concrete part, have a look at the attached image.
To explain the differences between the generic and concrete part, we chose a chemical-example. You can save information about a chemical (e.g. water) like the chemical structure or the molecular formula, but all these information are generic and equal for all kind of water you are using. If you have a bottle of water, you'll save concrete information like the amount of water, the manufacturer, the date of expire etc.
All in all we are intend to publish definitions of the names used in Open-LIMS and descriptions of each module.