Blog

We blog about genomics. We also make a platform for open-source analysis of next generation data in the cloud. Hello.

EU Safe Harbor Decision – Data Transfer Compliance Unchanged

A decision by the European Court of Justice on October 6th determined that the U.S.-EU Safe Harbor program provides inadequate protection for the transfer of European Union data subjects’ personal data to the United States. We take these issues extremely seriously at Seven Bridges. On behalf of clients, we monitor changes in the regulatory environment, and we go to great lengths to ensure ...
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Postcard from ASHG 2015

Predictions are a risky business. Advances in genome and genetic research – and some implications – were on display at this year’s American Society of Human Genetics conference (#ASHG15) with insights into the genome-based future of research and medicine. The Baltimore gathering showed how the massive volume of genome sequencing keeps producing new data sets, and prompting new questions ...
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From ASHG 2015, Dr. Wan-Ping Lee on a better read mapping graph

Last call #ASHG15. If bioinformatics and a better graph-based genome is your area of interest, you’ll want to meet Dr. Wan-Ping Lee of Seven Bridges Genomics at 3pm Friday 10/9 in Room 316. Here’s a brief introduction: Current short-read mapping algorithms utilize species-specific genome reference sequences to align reads from an individual. Many reads fail to map or are incorrectly mapped ...
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The 40-Year-Old Algorithm

Talk about job security. . . after 40 years, mathematicians have concluded that they cannot improve on the industry-standard algorithm used to compute the “edit distance” in analyzing long sets of digits or data. Decades of testing and analysis showed this to be a math problem with no solution, according to MIT researchers. The algorithm is used to compare two sequences with many common ...
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As scientists, we don’t just want to encourage data sharing — we want to measure it

There is a lot of talk of incentivizing data sharing in science, but which practices in particular do we want to encourage? At Seven Bridges, we have been thinking of how to design a metric that tracks the kinds of data sharing that most benefit science. Simply being a prolific sharer is useless if the quality or relevance of the data is poor. And sharing high-quality data is not helpful if ...
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Open Access Publishing Fees Are Reimbursed on the Platform

Just a quick note about something we expect many of our customers will appreciate: Seven Bridges now covers the open access publishing fees for any research paper that results from work done on our platform. As Deniz Kural, our CEO, put it: “We want to do everything possible to accelerate the pace of discovery.  Open is the next step of what we started with Rabix — our open-source ...
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Docker industry leaders unite to create an open specification for containers

I was happy to learn of the Open Container Project (OCP), announced yesterday. Docker, CoreOS, AWS and other major developers of containerzation technology will work together to create a single, open specification for containers that is not dependent on any particular architecture. While Docker has served us well in the development of our SDK, I’m looking forward to seeing what the OCP ...
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Docker-based solutions to reproducibility in science

Seven Bridges Genomics is launching a toolkit for creating fully portable bioinformatics workflows, based on Docker and the Common Workflow Language. With high-profile cases of data fabrication recently in the news, the New York Times asks how journal referees can detect fraudulent results in submitted articles when they are rarely given access to the raw data used in them. Generally, the ...
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Building a Cancer Genomics Cloud Pilot

An interoperable cloud platform to meet the next level of challenges in cancer genomics research We are delighted to announce that we were recently selected to participate in the Cancer Genomics Cloud Pilots project funded by the National Cancer Institute. The goal of this 24 month project is to democratize and speed cancer research by enabling all researchers to leverage cloud-computing ...
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On our way to ASHG!

Today, 10 excited members of the SGB team are on their way to (hopefully) sunny San Diego for this year’s American Society of Human Genetics (ASHG) meeting. With so many great presentations and sessions scheduled, it is sure to be a fantastic year for science at ASHG. It might be a little biased, given my background in virology, but in particular I can’t wait to attend Wednesday’s ...
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