Molecular Biology Software Streamlines DNA Cloning, Sequence Analysis and Visualization

Franck Perez didn't know he was going to be a software developer. Perez is a Cancer Researcher at the Curie Institute, a hospital that treats and researches cancer, in Paris, France. With a PhD in Genetics and Cell Biology, Perez's background is in Life Sciences. Perez uses his technical skills as a scientist, and his interest in understanding how things work, to create software to aid him and his colleagues to more efficiently do their jobs in the field of molecular biology.

When molecular biologists work on genes, they need to manipulate and modify DNA to prepare new DNA fragments for further use in gene and protein functional analysis. Perez and his team had been using an older application that was written in C called DNA Strider. Perez commented, "It is terrific software, but it only works on the Mac. This makes it hard to exchange files with Windows users and it does not provide any 'help for cloning' to automate certain steps when planning a construct." As a result, Perez decided to develop a small tool that would help him quickly plan a construct and that works well with DNA Strider files.

Perez created an application called Serial Cloner using Xojo, a cross-platform software development environment from Xojo, Inc. Serial Cloner allows researchers to manipulate, modify and prepare new DNA fragments via computer simulation before and during the cloning and sub-cloning stages. It mimics what a researcher would be doing on the bench and provides a reactive interface so they can plan and analyze cloning projects.

Powerful graphical tools and simple interfaces help the analysis and construction steps (adaptor, PCR, Gateway) in a very intuitive way. Version 1.3, which is available now, has a virtual cutter window, can generate silent restriction maps, and contains a Web browser allowing instant import of NCBI/EMBL sequences.

Perez found Xojo while he was looking for a way to develop native applications for his Mac. With little programming experience, he learned Xojo very quickly and taught himself by reading articles and studying code examples from magazines and on the web. He learned more by working directly in Xojo and creating his own applications. "When I go back to older parts of my code, I realize how much I have learned since," said Perez.

"With Xojo, I can quickly develop professional, multi-platform software," commented Perez. "In many cases, a researcher might be exchanging files between Mac and Windows platforms, which Serial Cloner supports thanks to Xojo."

In addition to Serial Cloner, Perez has also developed a simulation application with Xojo that was used in association with an article published in Science. He has also used Xojo for personal application development.