You are here: HomeScience OverviewArchive › Core Facility Management

Core Facility Management

A Customized Web-based Toolbox for Managing Microscopy Core Facilities

Nov. 28, 2011
Fig. 1: Schematic illustration of the toolkit modules, together with their interactions. The main page of the MCF website is written in HTML with CSS, whereas main webforms are in ASPNET, with the code-­behind in C#. The dynamic content is supported by Javascript, relying on jquery and jqueryUI. We set up both an IIS and an Apache webserver [3], in order to provide maximum flexibility for applications written in multiple languages. Our ASPNET webforms run on IIS by default, but we are also able to assign them to the Apache server via using the Mod_AspDotNet library [4]. Security is provided by the “.htaccess” and “.htpasswd” structure, with .htpasswd placed above the root folder for security reasons. The entire website is only available from within the Campus network or via a VPN connection, which further increases security.
Fig. 1: Schematic illustration of the toolkit modules, together with their interactions. The main ... more
Fig. 1: Schematic illustration of the toolkit modules, together with their interactions. The main ... Fig. 2: New users’ data are entered via a webform that was written in ASPNET using MS VS2008, with ... Fig. 3: The user database (DB) is in MS Access “.mdb” format and was assembled according to the ... Fig. 4: The Contact Form provides e-mail access to all equipment users groups and to the MCF staff, ... 

Managing an imaging core facility with numerous microscopes and many ever-changing users requires tools that track user contact and project data, allows easy communication between facility users and staff, and monitors the performance of the microscopes. Commercial tools are too general for these specific tasks, thus we developed a customized Core Facility Management tool-box that includes a user database, online user registration and contact forms, booking and trouble ticket system and a Wiki.

In order to efficiently manage our imaging core facility, we developed a custom-written web-based toolkit which allows prospective Microscopy Core Facility (MCF) users to register and apply for training, to contact various user groups via e-mail, to book equipment time as well as to provide facility managers with information about technical problems arising in the facility. The MCF toolkit consists of Registration, Booking, Contact Form, Trouble Ticket, Wiki Info and Administration are­as (fig.1). We used several programming languages and web-application toolkits that best suited our purposes. The website runs on a Windows Server 2008 R2 machine, dedicated to our Facility exclusively that is also used to store imaging data and to access floating licenses of image analysis software.

User Registration, Management of User and Project Data

New applicants who would like access to MCF services are required to fill out our user registration form (fig.2), which we run as a webform accessible from the MCF home page (for internal users). Via this form we collect user contact data and acquire first information about the intended microscopy projects. User registration data are automatically stored in our custom-written user database (DB, fig.3), which is password protected and is only accessible directly by MCF managers. Upon registration of a new user, the MCF staff is automatically informed via email. Already registered users can login with their password and change their user data or inquire for additional training sessions or access to additional microscope systems.

The user DB is the core of the management toolkit, and is thus backed up daily by our IT department as part of the server backup schedule.

In addition, we also keep an off-line copy of every updated version of the main DB. Direct access to the DB is provided for MCF staff via the Administration area. Here we can assign users to specific microscopes, get user groups statistics, and give access to specific microscope rooms via an automated email system that relays the request to the appropriate department.

Communication Between Facility Users and Facility Staff

In order to establish an easy and always up-to-date contact between the ever-changing microscope user groups and the MCF staff, we utilize our user database to support an on-line Contact sheet (fig. 4). Communication to specific microscope user groups and to MCF staff is provided via email distribution lists that are created automatically from the user database and are arranged by the microscopes. This contact form is used to announce free microscope time, hardware and software problems, repair schedules, etc.

In order to encourage users to inform the MCF staff about hardware and software issues at the MCF, and to facilitate communication between users and staff, we added an online Trouble ticket system called "osTicket" to our website. This is an open source ticket system that is very easy to set up and manage [1]. The new ticket is sent to all facility staff, it can be assigned to a specific person and is closed when the problem is solved. We also utilize osTicket to track our system repair history. Users can also follow the process of the issue that they raised in their trouble tickets.

We wanted to provide interested users with up-to-date information about the facility and the systems. We decided to use DokuWiki for this purpose, because it is easy to set up, it is very flexible, and we were able to customize it with plugins to provide extra features. The official DokuWiki page can be accessed at [2], where readers will find further information about the wiki, together with set-up instructions. Our DokuWiki runs on the Apache webserver and it contains information about how to get access to the facility, our user guidelines and a brief introduction to every system as well as the configuration and components of each of our microscope systems.

For Booking of MCF systems we use a Google calendar at the moment. Our plans include to assign automatic account and equipment access by linking a booking system's database (e.g. MySQL) to our user database via LDAP, and to synchronize their content.


These web-based tools simplify both ours and our users' everyday tasks of managing and using the facility. They make the administrative tasks of the facility staff more time-efficient, the access of users to the facility easier and more transparent. They ensure better contact between facility users and staff, which leads to a more efficient individual user support and faster troubleshooting.


Related Articles :

Keywords: Facility Management Imaging Core Facility Microscopy

Email requestCompany Homepage

Max-Delbrück-Centrum für Molekulare Medizin (MDC)
Robert-Rössle-Str. 10
13125 Berlin

Tel: +49 30 9406 0
Fax: +49 30 9494161

RSS Newsletter