Researchers at Department of Medical Biochemistry of the Semmelweis University are examining the
presence of mitochondrial proteins in healthy and tumorous tissues. Their aim is to develop
cancer-specific therapeutic methods by modifying bioenergetic processes in the human body. Dr.
Christos Chinopoulos, lead of the project, has sketched the concept of a software for supporting
their work. Pragmapill Ltd. has designed and realized LIBRA (Laboratory Information system of
the
Budapest Reverse phase protein Array facility) based on his imagination. Briefly they solubilize
human tissues to be able to print 5000 dots of them on a special slide. They stain the slide
with an
antibody and based on the size of the spots they determine the amount of a particular protein in
a
given sample. A detailed and more precise description is available at http://rppa.hu. Our software covers the whole workflow, starting from
tissue
collection, through the laboratory processing of the samples, to studying the results.
LIBRA is an SaaS product, hosted on IIS which is capable for serving multiple users at the same
time
with different privileges. The data is stored in MSSQL database, the business logic is
implemented
in .NET and services are exposed on a Web API interface. The thin-client is built with help of
various modern web technologies. The product has been delivered in two phases.
In the first phase we have implemented the modules needed for tissue collection. The collection
of
samples had been started before the needed laboratory equipment has been procured. A sample
involved
in the examinations has to fulfill strict preconditions, and has to be categorized based on
multiple
aspects. For example International classification of diseases for oncology (ICD-O) is available
in
the system and the appropriate ICD-O code has to be selected for every tumorous tissue. Some
Hungarian specimens are identified by social security number which is a sensitive information
and
has to be hidden from the users and stored encrypted in the database. On the other hand system
must
recognize if samples belong to the same patient and associate them. As Department of Medical
Biochemistry works with sites from all over the world, we made the system capable to work with
their
secret patient codes as well. Bulk data can be imported from well formed excel sheets. The
samples
are stored in barcoded tubes on -80 °C either unprocessed or solved. LIBRA supports the
process
of solubilization as well as tube and other labware equipment tracking in the freezers and
fridges.
Parallelly to the sample collection, validation of the antibodies has started. Antibody
administration is also part of LIBRA.
Modern laboratory machines are equipped with CPU and memory, capable to process digital input
and to
produce digital output. The second phase of LIBRA development was mainly about interaction with
these machines. The software interacts with Eppendorf's pipetting robot, with Aushon's arrayer
and
with MAPIX microarray image analysis software, generating them the files needed, and processing
the
data their run resulted. This way LIBRA covers the whole workflow needed for the stuff of the
department to quantify the amount of protein in tissues, contributing a bit to their effort on
beating cancer.