Pragmapill - Pragmapill

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.