Immumetrix
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Immumetrix analyzes DNA sequences and immune system data using advanced computational techniques to improve understanding of human DNA, particularly in transplant rejection cases. Compassites developed a cloud-based application that automates data processing, significantly reducing the time required for analysis from a week to hours while enabling parallel processing of tasks. The solution involves algorithms written in C++ and Python, producing outputs in both CSV and graphical formats.
Immumetrix
- 1. ImmuMatrix Business Situation Immumterix does analysis of DNA sequences and the immune system using Client Profile multiple lab techniques. They needed to use computational techniques to analyze DNA through methods like high throughput analysis. They would analyze the DNA Immumetrix is an early sequence and would represent each element through ASCII values. By studying stage biotech company at the DNA sequence thoroughly, they were able to understand human DNA through Palo Alto. Their focus is various algorithms. What they needed was sequence alignment analysis and on DNA in the immune similarity searches in biological databases. Each sample would contain system and they work on approximately 400 MB to 1 GB of data and would need customization based on health related projects the data collected. The need was to coordinate with the scientists from such as non-invasive Immumetrix in order to understand the complexities and align the analytical monitoring of organ algorithm accordingly. The objective of the project was to analyze the DNA data transplant rejection. More and provide outputs in CSV and graphical formats. details about them at www.immumetrix.com Solution Approach Immumetrix needed an application that would analyze the matches in the DNA sequences and produce the output of these analysis as charts. The studying of DNA and matching of certain sequences helped to identify if anti bodies were present and hence judge the possibility of certain types of diseases. Compassites did an initial data analysis of the data that was currently in the system. We did multiple reads of barcodes, isotypes and primers. We aligned sequences using concepts such as local alignment and dynamic programming. Some of the processing revealed details such as ‘primary antibody repertoire’ and the amino acid usage. The tool built by Compassites was on the cloud. We created an Excel file where the scientists had to simply add their data in a DropBox. The application would go onto read this Excel sheet and get to know what data had to be processed. Post processing, the results of the analysis was dumped back into the DropBox folder. You can read more Reach out to us at Via email about Compassites at +91 - 80- 4203 2572 info@compassitesinc.com www.compassitesinc.com +91 - 80- 6500 2371
- 2. The algorithms of Immumetrix were written in C++ and Python. The application created by Compassites generated charts using the Python MatPlotLib library. Compassites used Gearman for parallel processing of the data. Technology Used C++, Python, PHP, HipHop PHP, Biopython, Matplotlib, Gearman and pdftk Benefits & Results The early system used to take a week to do the processing of the data. The current system does it in a few hours. With the new system, a lot of processes can be done parallelly instead of in serial order. Compassites helped to improvise the code and the algorithms in order to make them run faster. Initially there were a lot of manual tasks to be done in order to run each program. Now a lot of the tasks are automated. Since the application is on the cloud, Immumetrix is also paying "by use" and is not having to pay for physical hardware and servers at their location. Bangalore Center Pune Center "Gaayatthri Chambers", #948, 24th Main Rd,2nd Phase, 608 - Kapil Zenith Building, Near Chandani Chowk, J.P.Nagar, Bangalore - 560078 Karnataka, India Off Bangalore - Mumbai bypass, Bavdhan, Pune - 411021 Phone: +91 -80 42032572 Maharashtra, India Phone:+91-20-6500 2371