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The Prefix Burrows-Wheeler Transform (PWBT) is described to provide data operations on data sets even if the data set has been compressed. Techniques to set up a PWBT, including an offset table and a prefix table, and techniques to apply data operations on data sets transformed by PWBT are also described. Data operations include k-Mer substring search. General applications of techniques using PWBT, such as plagiarism searches and open source clearance, are described. Bioinformatics applications of the PWBT, such as genomic analysis and genomic tagging, are also described.


Systems and methods to create a merged lexeme set from a first lexeme set and a second lexeme set such that an existential lexeme search may be performed on both data originally from the first lexeme set and data originally from the second lexeme set via the merged lexeme set, and wherein information in the merged lexeme set includes information as to which lexeme set a lexeme originated. Specifically Prefix Burrows-Wheeler Transform (PBWT) systems and techniques are applied to the scenario where a plurality lexeme sets are merged to a single merged lexeme set. Additionally, applications of PBWT systems and techniques as applied to genome sequence data and k-Mer searches are disclosed.


The Prefix Burrows-Wheeler Transform (PWBT) is described to provide data operations on data sets even if the data set has been compressed. Techniques to set up a PWBT, including an offset table and a prefix table, and techniques to apply data operations on data sets transformed by PWBT are also described. Data operations include k-Mer substring search. General applications of techniques using PWBT, such as plagiarism searches and open source clearance, are described. Bioinformatics applications of the PWBT, such as genomic analysis and genomic tagging, are also described.


The current document is directed to a method and system for data processing in cloud-computing environments and other distributed-computing environments. Implementations of a merge sort suitable for the sorting of data within cloud-computing environments and other distributed-computing environments are disclosed. These implementations takes advantage of the massive parallelism available in cloud-computing environments as well as take into consideration numerous constraints regarding data-storage and data-retrieval operations in a cloud-computing environment. The implementations provide a type of data-sorting method and system that iteratively carries out highly parallel merge-sort operations that can be effectively applied over a range of data-set sizes up to extremely large data sets.


Patent
Spiral Genetics | Date: 2015-02-25

DNA assembly techniques for a DNA dataset comprised of DNA sequence reads make use of anchor points identified using a reference DNA sequence. Because the anchor point technique is dependent on a high accuracy dataset, related techniques to detect erroneous reads and to correct erroneous reads making use of k-Mer and statistical techniques are also disclosed. Upon preparing a high accuracy dataset, a read overlap graph is generated that removes exact matches with respect to the reference DNA sequence, thereby leaving behind potential structural variants. Using anchor points representing closed matches to the reference DNA dataset, the read overlap graph is traversed to detect potential structural variants. The structural variants are then validated. Use cases for anchor assembly and related techniques, including multi-sample differential variant detection are also disclosed.


The current document is directed to automated methods and processor-controlled systems for assembling short read symbol sequences into longer assembled symbol sequences that are aligned and compared to a reference symbol sequence in order to determine differences between the longer assembled symbol sequences and the reference sequence. These methods and systems are applied to process electronically stored symbol-sequence data. While the symbol-sequence data may represent genetic-code data, the automated methods and processor-controlled systems may be more generally applied to various different symbol-sequence data. In certain implementations, redundancy in read symbol sequences is used to preprocess the read symbol sequences to identify and correct symbol errors. In certain implementations, those corrected read symbol sequences that exactly match subsequences of the reference symbol sequence are identified and removed from subsequent processing steps, to simply the identification of differences between the longer assembled symbol sequences and the reference sequence.


Systems and methods to create a merged lexeme set from a first lexeme set and a second lexeme set such that an existential lexeme search may be performed on both data originally from the first lexeme set and data originally from the second lexeme set via the merged lexeme set, and wherein information in the merged lexeme set includes information as to which lexeme set a lexeme originated. Specifically Prefix Burrows-Wheeler Transform (PBWT) systems and techniques are applied to the scenario where a plurality lexeme sets are merged to a single merged lexeme set. Additionally, applications of PBWT systems and techniques as applied to genome sequence data and k-Mer searches are disclosed.


News Article | October 23, 2015
Site: tech.co

Knowing when to scale is the single most important reason for startup success. Janis Machala of Paladin Partners says that market timing is the biggest reason by orders of magnitude. This part is more art than science and is a function of product market fit. Ahead of her panel during Seattle Startup Week, she chatted with me about this topic and the people on the panel who are the best examples. Janis Machala is the managing partner of Paladin Partners. Paladin is a consultancy firm based in Kirkland, WA founded in 1995 focused on start-up growth and team building. Janis is moderating a panel on Monday Oct 26 at Seattle Startup Week called Making B2B Companies Scale: Women Entrepreneurs Weigh In. The four speakers on the panel each overcame unique issues in building their own companies: Janis also recommended reading Four Steps to Epiphany by Steve Blank. She says she wishes she had written this book, and that every client she has ever served should read it. Here is a PDF of a shorter presentation on the book. Additionally, Janis recommends founders read this article by Mark Leslie to learn more about how to scale their startup and why. Janis says market focus must be as narrow as possible in the beginning, and once you have nailed the sales in one area move to the next. In each step of growth, it’s vital to focus your time as a founder and CEO interviewing users, identifying pain points, and adjusting the product to fit. Janis said you must listen more than you talk if you want to succeed. This is where Janis feels women have an advantage over men. “Women are better listeners than men,” she said. Janis acknowledged the broad generalization there, but that statement is not without truth. Janis has the business chops to make such a conclusion. Her background is solid and results are impressive. Janis will also be hosting a B2C panel on scaling on Friday, Oct. 30. There is value in the panels she is hosting. Janis said she wanted to have distinct panels for each segment as there are issues inherent to the markets that don’t cross over. Seattle Startup Week runs Oct 26-30 in downtown Seattle and many other locations in the area.


News Article | March 12, 2013
Site: gigaom.com

Spiral Genetics, a Seattle-based startup that helps researchers and others quickly analyze DNA sequence data, has raised $3 million in its first institutional round of funding. The Series A round was led by venture firm DFJ and brings the startup’s total amount raised to $3.7 million. With the new funding, Adina Mangubat, Spiral Genetics co-founder and CEO, said her eight-person team plans to expand product development, as well as sales and marketing. Mangubat said that when she and one of her co-founders, Becky Drees, first looked at the field of genomics, their plan was to launch a consumer-focused genetic testing service like 23andme. But as that company started launching its services, they decided to switch tacks. “We were looking at the industry and we wanted to do something really impactful that involved genomics and computing,” she said. When they realized the speed and volume with which raw sequence data was being generated, she said, they spotted an opportunity in offering high-performance bioinformatics tools for analyzing it. Companies like DNANexus also offer sequence analysis, and others might conduct the analysis in-house, but Mangubat said they envisioned a service that could shrink the turnaround time for researchers and others in industry deluged by data. Last month, Redwood City, Calif.-based Bina Technologies announced the commercial launch of its own genomic analysis platform and similarly touts a faster-than-ever service. Mangubat and Drees teamed up with their third co-founder Jeremy Bruestle and started building a computing platform specifically intended to solve this kind of big data problem. Now, the company says, it can analyze a whole human genome in 3 hours, which is about 40 times faster than what it might take others. Spiral Genetics’ customers run the gamut from academic researchers to corporations, Mangubat said. For example, while some clients may use their bioinformatics tool to tackle childhood cancer, others in agrigenomics could use it to sequence different strains of corn. Along with the new funding, Spiral Genetics announced a new partnership with Omicia, an Emeryville, Calif.-based provider of clinical genome sequence interpretation tools.


News Article | April 20, 2015
Site: www.geekwire.com

Next up in the GeekWire Awards voting is one of our favorite categories: Young Entrepreneur of the Year. Youth is not wasted on the young, at least when it comes to these inspiring entrepreneurs, all of whom have achieved amazing things at the age of 30 or younger. Some have asked us why we even recognize young entrepreneurs, but the answer is simple. A thriving tech ecosystem needs a pool of new entrepreneurial candidates who can usher in change, seeing around corners and ushering in disruptive technologies. This year’s class of finalists certainly achieves that. (See below for voting and short descriptions). If you’re just tuning in, we’re in the midst of picking the winners in 13 categories — ranging from Startup of the Year to Innovation of the Year to Geek of the Year — as part of the annual GeekWire Awards. Over the next few days, we’re opening voting in each of 13 categories, with GeekWire readers choosing their top picks. All of the winners will be revealed at the GeekWire Awards — presented by Wave Broadband — on May 7 at EMP. A big thanks to OfferUp, the presenting sponsor for this year’s Young Entrepreneur of the Year category. Vote in the poll below, and keep reading for descriptions of each of our five finalists this year. Gilad Berenstein of Utrip: After launching its online travel service last April, Utrip continues to grow under the direction of 27-year-old CEO Gilad Berenstein. The company is adding new users each month, and while Berenstein says revenues are small, they are starting to grow. The company raised $1.6 million last year, and now employs 11 people. Berenstein came up with the idea for Utrip after traveling in Europe following grad school, noting that travel books just weren’t good enough to help craft his experience. The University of Washington grad wondered if a more personalized experience could be created, without the high costs of a travel agent. Aviel Ginzburg of Simply Measured: Aviel Ginzburg’s LinkedIn bio kind of says it all: “Product obsessed workaholic.” Yes, those are traits of successful entrepreneurs, and Ginzburg has made his mark as the co-founder of Seattle-based Simply Measured. The social media analytics company has grown from a germ of an idea when he and co-founder Damon Cortesi started it under the moniker “Untitled Startup” five years ago. The 30-year-old Ginzburg, who studied economics at Vanderbilt University, has helped grow the team to more than 150 employees. It raised $20 million in venture funding last year, and today the social analytics tool is used by companies such as Pepsi, Microsoft, Whole Foods and Adidas. Josh Neblett of etailz: Spokane entrepreneur Josh Neblett started etailz seven years ago after hearing a venture capitalist pitch an idea at Gonzaga University for an online eco-friendly retailer. Today, the company Neblett co-founded along with venture capitalist Tom Simpson operates five niche e-commerce sites, including Ecomom, GreenCupboards and EveryCasa. Neblett, 28, has never slowed down since starting the company. The company has used its profits to expand, growing the business each year. In 2013, etailz ranked #128 on the Inc. 500 list with revenue of $13.1 million and a 3-year-growth rate of 2,898 percent. It landed there again in 2014, ranking #313, with annual 2013 annual revenue of $27 million. Adina Mangubat of Spiral Genetics: Spiral Genetics CEO Adina Mangubat is helping to develop technologies that could make each of us healthier. The bioinformatics company she co-founded six years ago is developing software for complex DNA analysis, The company’s flagship product, known as Anchored Assembly, utilizes high performance computational algorithms to identify genetic structural variants. The company is backed by venture capital powerhouse DFJ, and the 28-year-old Mangubat continues to lead an ambitious effort at the life sciences upstart. “Our goal is to produce software that harnesses the potential of large-scale genome sequencing and can usher in the era of precision medicine,” said Mangubat in a recent release. Ryan Vogel and Adam Greenberg of Pure Blue Tech: Adam Greenberg, 25, and Ryan Vogel 23, are assembling some of the top thinkers in the world when it comes to water treatment. The University of Washington grads also have inked an alliance with WaterTectonics, a global water treatment manufacturer for the oil, gas and mining industries. Still in its early stages, Pure Blue nonetheless is looking to solve a big problem, boosting water supplies by developing a system that reduces the cost of desalination. In 2013, the company won the University of Washington Business Plan Competition, with Vogel saying at the time of the award: “The vision is to create an A to Z water treatment solution that will allow us to convert any water in the world …. into pure potable water for drinking or other purposes.” Don’t forget to grab your tickets for the GeekWire Awards. This event usually sells out. And this year, things will be especially geeky as we open up the amazing Star Wars costume exhibit at EMP to all GeekWire Awards guests. What better way to get your geek on than go face-to-face with Chewbacca!

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