Benchling, which provides DNA editing and analysis software, and New England Biolabs, a leader in the production of enzymes for genomic research, have entered into a collaboration to facilitate the design of cloning experiments. The companies are launching a free online tool to assist researchers working with the Golden Gate DNA assembly method.NEB and Benchling's tool will simplify experimental design for their customers: the user inputs the DNA fragments of interest, and it simulates the reaction, designing the primers and generating the final DNA construct. The design process is optimized to minimize errors, and the user downloads a protocol with the appropriate Golden Gate Assembly reaction.

Benchling was founded by former iGEMers advised by Ron Weiss of the MIT Department of Biological Engineering.

Sajith Wickramasekara, co-founder and CEO of the company told us that “Benchling was started by a group of software engineers with molecular and computational biology experience. Many of us chose not to pursue paths in science because we were frustrated at how hard it was to work together. We’ve experienced the pain of poorly managed data, irreproducible research, and paper lab notebooks.”The company is backed by about $900,000 from Y Combinator, FF Angel, SV Angel, Draper Associates and others. It was the first synbio company to be funded by Y Combinator, back in 2012. Sajith also told us that the company has exciting announcements lined up for 2015, ranging from collaborations to new products designed to serve scientists.Advances in cloning technologies are making synthetic biology research more efficient and collaborative. As the costs of DNA synthesis and sequencing drop rapidly, more advanced cloud-based software for biotech labs come in handy, reducing the time and costs required to carry out experiments. Benchling’s customers are working on food safety, vaccine development, gene therapy, drug discovery, biofuels, genetically modified crops, and more. The company has also developed genome engineering solutions to automate the design of CRISPR plasmids, and it offers an open source tool that counts the number of colonies in a petri dish.

Benchling can automate colony counting: by uploading the plate image to Benchling it will process it and return your counts back. Source: http://blog.benchling.com/automate-your-colony-counting/