[Editors note: Architect Robert Noble wrote this article with Glenn Croston]

The San Diego area is the home of numerous cleantech businesses that are developing innovative green cars (Aptera, V-Vehicle Co.), developing alternative fuels (GreenHouse International, Synthetic Genomics Inc., Sapphire Energy), finding alternatives to petrochemicals (Genomatica, Verdezyne), and providing renewable energy and energy efficiency solutions (KEMA, Kyocera, Envision Solar).

Assisting our growing cluster is a network of non-profits, trade groups, government agencies, universities, and investors who share a common interest in cultivating a green economy. These groups collaborate on many projects, strengthening our vision for more green businesses, jobs, and investments in cleantech innovation. But while they share common goals, local green groups are also distinct in many ways and often compete for money, members, and media; their varying perspective, focus, message, membership, and goals can be confusing. If you’re an entrepreneur, how can you find support for the green innovations you hope to commercialize? Where do investors look for opportunities and advice? Where can founders find the resources they need to move their ventures forward?

We’ve compiled a listing of these groups to help San Diego entrepreneurs and others find the resources they need to grow green, and to help San Diego’s green economy grow.

—The California Center for Sustainable Energy (CCSE) is the cornerstone in developing San Diego’s green business cluster. As a non-profit, the CCSE works to advance the adoption of renewable energy, green building design, clean transportation options, and energy efficiency by providing workshops, information, and training.

—Cleantech San Diego is a membership-based non-profit industry association that sponsors events for businesses, investors, and others working in the cleantech cluster. They summarize their mission on their website, saying, “Cleantech San Diego advocates for new sources of investment capital, workforce development, international trade, federal and state research funding, targeted regulation, and sustainable land use planning and development.”

—San Diego Clean Enterprise Program, which is administered by Cleantech San Diego through a partnership with the City of San Diego and the mayor, which provides interest-free financing for energy efficiency improvements for small businesses. Cleantech San Diego also is working with the rest of the green community to support funding and grant applications, such as the effort to win $260 million in Clean Renewable Energy Bonds (CREBs) for local solar projects.

—San Diego Gas & Electric committed to develop a distributed solar power generation system in the San Diego region in 2008. So it’s no surprise that …Next Page »

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After Carlsbad, CA-based Verdezyne disclosed last month that it plans to raise more than $15 million in venture funding, I arranged to sit down with Damien Perriman, the company’s vice president of business development.

As it turns out, the startup that was founded in 2005 as CODA Genomics has essentially re-engineered itself over the past 18 months. The company overhauled its core business strategy, recruited a new CEO, E. William Radany, along with a new management team, changed its name, and moved its headquarters from Orange County to Carlsbad, CA, about 28 miles north of San Diego. In changing its name to Verdezyne, the company created an identity that is better aligned with its revised focus on the “green design” of biofuels and industrial chemicals.

The company initially was focused on technology spun out from UC Irvine that used specialized computer algorithms to design synthetic DNA. The company offered its services in Computationally Optimized DNA Assembly, or CODA, to help drug discovery teams at pharmaceutical customers like Eli Lilly and Genentech design synthetic genes that could be used to maximize the production of certain proteins for their biotech drug manufacturing processes.

Perriman, who joined Verdezyne in February, tells me, “Our investors made a decision in 2008 that we could make a lot more money by doing the production ourselves.”

With its extensive experience in computational biology and bioinformatics, Verdezyne saw the value in creating high-diversity libraries of genes, so that various genes could be inserted into fast-dividing yeast cells (and other micro-organisms), essentially programming the microbes to produce enzymes it would not otherwise produce. Verdezyne landed a federal grant last month to help build out its genomic library.

“We prefer to work with yeast,” Perriman says, “but we can work with any fungi or bacterial organism.”

The company, which now has 26 employees, has identified three primary markets for its technology.

The first and most obvious target is an …Next Page »

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Aptera, the sleek carmaker backed by Google and Idealabs, didn’t respond to my inquiry earlier this week about reports of an internal split in which founders Steve Fambro and Chris Anthony had left the company. But in an online report published today by The San Diego Union-Tribune, Aptera officials rejected accounts that Fambro and Anthony were ousted in a boardroom showdown.

The company’s status is a keen issue to some 4,000 people, including celebrities Tom Hanks, Robin Williams, and Shaquille O’Neal, who have put down $500 deposits to be the first to buy one of the three-wheel, two-seater vehicles. The Aptera 2e, the company’s first production vehicle, resembles a wingless plane and is expected to cost between $25,000 and $40,000. Aptera is based in Vista, CA, about 30 miles north of San Diego.

Citing a statement issued by Aptera CEO Paul Wilbur, the Union-Tribune says the carmaker had to adjust its production schedule “to align with financing realities.” Instead of producing its first fuel-efficient model in the fall of 2009, as Aptera announced at the beginning of this year, Wilbur says the company will complete its first vehicles in 2010. About 10 of Aptera’s 40 employees have been laid off.

The company, which has raised at least $27.5 million from Google, Idealabs, and other venture investors, is seeking additional funding, according to Popular Mechanics. Aptera says it also intends to resubmit its application for a $75 million loan from the Department of Energy’s Advanced Technology Vehicles Manufacturing Incentives Program.

Aptera says co-founders Fambro and Anthony were not asked to leave. Fambro remains on the board, but has taken a leave of absence from the company until next year. Anthony is now the CEO of Flux Power, a startup in the San Diego area that is developing battery-management systems. In another online account published by Popular Mechanics magazine, Fambro also voiced his continuing support for CEO Wilbur.

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As startups developing next-generation biofuels emerge in San Diego, Boston, and elsewhere, a business model for rapidly expanding to commercial-scale operations already can be found in the biotech industry, experts said yesterday. The premise of presentations organized by Biocom, San Diego’s life sciences industry group, is that collaborations being formed between biofuel startups and big energy are comparable to the partnerships formed between biotech startups and big pharmaceutical companies.

Biofuels development partnerships will be crucial to meeting renewable fuel standards that the federal government set in the Energy Independence and Security Act of 2007. Wain Fishburn, a founding partner of the Cooley Godward law firm’s San Diego office, said the standards require the U.S. biofuels industry to increase its production fourfold—from 9 billion gallons in 2008 to 36 billion gallons in 2022. Fishburn, who introduced the speakers at the Biocom event, said the ability to meet the federal goal depends on a variety of factors, including the ability to lower the cost of biofuels to be competitive with petroleum-based crude, and the scalability of feedstock, production facilities, distribution, and related infrastructure.

But what it really comes down to, as Verenium (NASDAQ: VRNM) executive William Baum told the audience, is capital.

Baum, who became Cambridge, MA-based Verenium’s executive vice president of business development in 2007 (following the 2006 merger of San Diego’s Diversa and Cambridge’s Celunol) said the need for capital was the theme he heard “over and over again” during a recent meeting that focused on the biofuels industry. “We’ve got hundreds of biofuel companies that are trying to get to the next stage. If you don’t have a big brother with deep pockets, like a BP, Exxon, Shell, or a Chevron, it’s going to be very difficult.”

A number of partnerships already have been established between biofuels startups and major energy conglomerates, Fishburn noted. He listed the following collaborations:

—BP, the London-based global energy conglomerate, has formed two strategic partnerships with Verenium, which has been developing technology to produce cellulosic ethanol using proprietary microbes to accelerate the breakdown of non-edible, high-cellulose plant material into ethanol. Baum described the first collaboration, announced in August 2008, as a technology joint venture for IP. (BP agreed to put up $90 million to develop “low-cost, environmentally sound cellulosic ethanol production facilities in the United States.”) Through a second deal announced nine months ago, BP agreed to provide an additional $45 million and to form a …Next Page »

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Long before San Diego was known as a hub of telecommunications innovation or for its proliferation of biotech companies, it was a leading center for the development of deep underwater technologies.

During the 1960s and ’70s, scientists from the U.S. Navy laboratories on Point Loma and UCSD’s Scripps Institution of Oceanography founded numerous startups with technologies derived from underwater sensors, acoustics, and signal processing techniques that had been developed for the Navy’s cat-and-mouse games with Soviet submarines. Robotic technology that the Navy had developed to recover a hydrogen bomb from the bottom of the Mediterranean Sea in 1966 led almost directly to the formation of Hydroproducts and Ametek Straza, two companies that made deep ocean ROVs (Remotely Operated Vehicles) in San Diego during the 1970s. Hydroproducts and Ametek Straza faded from San Diego, however, after they were acquired by bigger companies that wanted to introduce ROVs to the offshore oil and gas industry.

It might not be apparent on the surface, but much of that expertise in subsea technologies remains in San Diego today, according to Leonard Pool, who founded Sidus Solutions in 2000 to develop deep underwater pan-and-tilt camera systems and related ROV positioning equipment. Pool, who is moderating a panel discussion today on “marine technology as an important growth industry” for San Diego, says close to 150 companies continue to ply their trade here.

Alvin Diving off California

“When the U.S. Navy decided that San Diego was going to be a port for submarines, all these companies sprang up,” Pool tells me. “We do get looked at as a cottage industry.” He says these companies have thrived, despite a post-Cold War decline in defense funding for new submarine-hunting technologies. One likely reason, Pool says, is that the “oil and gas community continues to look at San Diego as a hub for subsea technology development.”

Pool’s panel discussion is part of “The Maritime Collaboration Summit,” a two-day conference organized by the Maritime Alliance, a San Diego non-profit industry group, aboard the tourism ship Inspiration Hornblower. The summit, which ends today, is intended to increase awareness of San Diego’s importance as a hub for technology innovation, and to encourage collaboration between the scientific community and commercial maritime innovators, according to Michael B. Jones, president of the Maritime Alliance.

“Right now, the maritime community in San Diego is very fragmented with little visibility or public understanding of its importance,” says Jones, who also heads …Next Page »

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GenVault wants to bring biological samples in from the cold. For decades, the biological samples used to diagnose or study disease have been stored in freezers, which use a lot of electricity. GenVault markets dry-storage technologies that allow scientists to store samples—such as DNA from a blood test—at room temperature.

GenVault CEO David Wellis argues the company’s technologies free up lab space and are better for the environment. He says that one of GenVault’s desktop storage units can hold as many samples as an average-size lab freezer, which has the same carbon footprint as five automobiles. Freezers have another major drawback: a single power failure can destroy years of work.

Wellis says the time is right for his company. The use of genomic analysis for disease diagnosis, scientific research, and forensic criminal investigations is exploding, thanks in part to technical advances that enable the swift decoding of genes. All these genetic tests start with biological samples, such as blood, urine, or spit. The RAND Corp. recently estimated that more than 307 million tissue specimens are stored in the United States, with more than 20 million specimens added each year. That means more and more freezers are taking up lab space, and running up electricity bills.

GenVault, which is based about 26 miles north of San Diego, in Carlsbad, CA, estimates that sample transport and storage represents a $4.5 billion business opportunity. It is also an area in which innovation has been lacking. “All the technical development has occurred in sequencing and informatics,” says Wellis. “The management of samples has seen no innovation. It is a gaping hole.”

GenVault got started in late 2001 to fill that perceived hole. The venture-backed company has raised more than $32 million to date, and has numerous customers, including the national Centers for Disease Control and Prevention, Genome Québec, and Amgen. The company expects to soon announce a new diagnostic lab customer that expects to store 750,000 samples using GenVault’s technology. Wellis says GenVault, which has 40 employees, could breakeven by the end of next year.

The company markets two products. One is a chemically treated paper that preserves bits of whole samples, such as blood or spit; the other a salt-like mineral matrix that preserves purified DNA. Here is how GenVault says …Next Page »

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On May 18th of 2009, I signed the papers to legally incorporate my first company. Three weeks later, I graduated from MIT with my BS in biological engineering. Fast forward, and after 10 months of working on the venture, it was decided to not continue.

After failing to get the outcome the team had hoped for, some questions loom: did I make the right decision to jump into the entrepreneurial arena so early in my career? Is it generally a good idea to start a company right out of college?

Before I answer these questions with the benefit of hindsight, I’d like to first take you through the process that led to my decision to just go for it.

During the year prior to making this decision, I had spent a lot of time thinking about what I would do after graduation. I knew I wanted to be a part of the entrepreneurial community, so I began learning all I could about the entrepreneurial process. I read everything I could get my hands on, I talked my way into relevant MBA courses at MIT’s Sloan School of Management, I did projects for startups and venture funds, and I sought advice from members of the entrepreneurial community.

I received a variety of opinions on the best route for getting into the land of startups. Here are the three most common views, along with my brief analysis of each:

Go get a job. Learn how real business is done first. This is the safe advice, which is why it is the most prevalent. By getting work experience, you get a chance to really develop your network, expertise, and understanding of problems in a specific industry. However, working in a mature business isn’t anything like a startup.

Go work for a startup. “Startup” work environments, of course, vary heavily. Some startups are a couple of guys working out of their apartment trying to find a way to make some revenue. Others are more like developed companies, with office space, hours, and managers.

At the time, to me, joining a later-stage startup didn’t seem all that different from getting a job at a more mature company. Joining a smaller band of warriors setting out on the start-up road would have been difficult. In the early stages, such efforts mainly need engineers to get a prototype built. I knew how to code, but programming wasn’t my forte. All in all, this wasn’t a very good option in my eyes.

If it feels right, go do it. The negatives for starting a company immediately after school are the lack of experience, network, credibility, and money. But, there are many positives:

• Access to a lot of help. I find the entrepreneurial community to be incredibly supportive, with lots of vibrant, experienced people happy to help students. I had access to tons of great people through the MIT and Boston communities. I talked with professors, cold called and emailed alumni, and just found a way to get in touch with people. Not everyone would respond, but those who did were extremely helpful.

• Low opportunity cost. You aren’t walking away from a high-paying job in order to attempt a startup, so you have little to lose financially if it doesn’t work out.

• Low responsibility. By this I mean you …Next Page »

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I had an opportunity to sit down recently (along with several other journalists) for an informal chat with Ellen Pao, a partner at Kleiner Perkins Caufield & Byers and a member of the famed Menlo Park, CA, venture firm’s GreenTech investment team.

Pao was in town to be the keynote speaker at the inaugural Cleantech San Diego Showcase, an event the non-profit industry group intends to hold four times a year as a way of calling attention to emerging green technologies and the local companies developing them. Pao provided an overview of KPCB’s GreenTech team, which consists of 20 partners in the United States and China. The firm has invested about $680 million over the past five years in nearly 50 startup companies, most of which remain in stealth mode.

Pao was gracious, but not especially forthcoming. For example, she told us that KPCB’s greentech investments include funding San Diego-based V-Vehicle Co., which announced plans earlier this year to build a new line of “environmentally friendly and fuel-efficient” cars in Northeastern Louisiana. The green aspect of the V-Vehicle’s design apparently figures in the startup’s request for a $250 million low-interest loan under the Department of Energy’s Advanced Technology Vehicle Manufacturing program. But V-Vehicle has not explained publicly how or why its car is eco-friendly, which has led to conflicting media reports (with some describing it as an electric vehicle). But Pao declined to explain why V-Vehicle is green, saying KPCB doesn’t talk about portfolio companies that are still in stealth mode—even though partners John Doerr and Ray Lane participated in a news conference that Gov. Bobby Jindal of Louisiana held in June to announce the state’s support for the project.

Pao said KPCB’s cleantech investments are divided among startups that are focused in a variety of green categories, including energy efficiency, cars and transportation, batteries (especially companies developing new energy storage capabilities for electric utilities), renewable energy, and “carbon management and sequestration,” i.e., technologies for preventing carbon dioxide from wafting into the atmosphere by capturing the gas and piping it underground.

“There’s a lot of passion around trying to solve the global warming problem,” Pao said. “We’re looking, though, for big solutions. We have some projects, and we think it’s a big opportunity once there is a price on carbon.” She was referring to a “cap and trade” proposal put forward by the Obama Administration that would set strict limits on pollution that causes …Next Page »

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[Updated 11/16/09 6pm. See below] Microsoft co-founder and renowned technologist Paul Allen has been diagnosed with non-Hodgkin’s lymphoma, a form of cancer, as of early this month, according to an e-mail message sent from Allen’s sister, Jody Allen Patton, to employees of Seattle-based Vulcan and its affiliates this afternoon. The message was sent to Xconomy and other media outlets by a Vulcan spokesperson.

Doctors say Allen has diffuse large B-cell lymphoma, which is a relatively common form of lymphoma, and he has begun chemotherapy, according to the e-mail. The message pointed out that Allen “beat Hodgkin’s a little more than 25 years ago and he is optimistic he can beat this, too.” That form of cancer is different from Allen’s current diagnosis, which is classified as a non-Hodgkin’s lymphoma.

Non-Hodgkin’s lymphoma is an umbrella term for cancers in which white blood cells of the immune system start growing out of control, according to the National Cancer Institute. The disease is the fourth most commonly diagnosed cancer in the U.S. each year, following lung, bladder, and melanoma tumors, according to the American Cancer Society. About 66,000 new cases are expected to be diagnosed this year in the U.S., and about 19,500 people are expected to die from the disease. Diffuse large B-cell lymphoma is the most common subtype of non-Hodgkin’s lymphoma, accounting for 30 percent of all newly diagnosed cases, according to an expert review published by the Lymphoma Research Foundation.

Vulcan spokesman David Postman wouldn’t comment on any specific questions about the stage of Allen’s disease, how early it was detected, whether it is an aggressive or slow-growing form of lymphoma, or where he is getting treatment.

Those questions are key to determining what kind of prognosis Allen has. His form of cancer is generally considered an aggressive, fast-growing lymphoma and requires immediate treatment, according to the Lymphoma Research Foundation’s description, authored by Carol Portlock of Memorial Sloan-Kettering Cancer Center in New York, Julie Vose of the University of Nebraska Medical Center in Omaha, NE, and Bruce Cheson of Georgetown University Hospital in Washington D.C. The first sign is usually when the lymph nodes swell in the neck, armpit, or groin—other symptoms include night sweats, unexplained fevers, and weight loss, according to the summary from Portlock and colleagues.

A common treatment for the disease is a regimen of chemotherapy combined with Roche and Biogen’s targeted antibody drug rituximab (Rituxan), which kills excess B-cells of the immune system. The combination treatment can lead to a cure in a large number of patients. “Even when a cure is not possible, treatment can often keep the disease away for many years,” Portlock wrote.

“Paul is feeling OK and remains upbeat,” the Vulcan message stated. “He continues to work and he has no plans to change his role at Vulcan. His health comes first, though, and we’ll be sure that nothing intrudes on that.”

Here is the Vulcan e-mail in its entirety [added 11/16/09 6pm]:

.

To employees of Vulcan and affiliates:

I want to let you know that Paul was recently diagnosed with non-Hodgkin’s lymphoma.

He received the diagnosis early this month and has begun chemotherapy. Doctors say he has diffuse large B-cell lymphoma, a relatively common form of lymphoma.

This is tough news for Paul and the family. But for those who know Paul’s story, you know he beat Hodgkin’s a little more than 25 years ago and he is optimistic he can beat this, too.

Paul is feeling OK and remains upbeat. He continues to work and he has no plans to change his role at Vulcan. His health comes first, though, and we’ll be sure that nothing intrudes on that.

We would ask you to respect Paul’s privacy and not discuss this outside of the office.

If you have any questions, please ask your EC member.

Thank you in advance for what I know will be all your good thoughts for Paul.
Jody

.

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Paul Wilbur, a Detroit auto industry veteran who was named CEO of Carlsbad, CA-based Aptera 14 months ago, gave no indication of internal turmoil at the futuristic car’s headquarters when he appeared last week at an event sponsored by Cleantech San Diego.

But as Darryl Siry reports today on Wired’s Autotopia blog, a prolonged power struggle that pitted Aptera founders Steve Fambro and Chris Anthony against Wilbur and Aptera board members apparently came to a head in recent weeks. Wired says rumors about the founders’ departure, as well as layoffs amid financial difficulties, began appearing last week on the Aptera Forum, an online message board for Aptera car enthusiasts. Aptera did not immediately respond to an e-mail query seeking the company’s response to the reports. According to Wired, the company says it’s slowing down its burn rate while waiting for the Department of Energy to review its loan application, and maintains that its relationship with Fambro and Anthony remains positive.

Fambro, who founded Aptera about six years ago, has previously said his aim with the company was to build a safe and comfortable passenger vehicle that was more fuel-efficient than anything else on the road. The company says the prototype of its aerodynamic pod-shaped, three-wheel vehicle gets 230 miles to the gallon.

Aptera raised about $24 million roughly 18 months ago from investors that include Google and Idealab. CEO Wilbur told me last year that the company was having no trouble attracting additional funding, but the Wired blog reports that additional funding has in fact been difficult to secure during a drawn-out battle over which course the company should be steering.

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San Diego’s Global Analytics Holdings says it has raised $10 million of a targeted $14 million round that consists of equity investments, options, and rights to securities, according to a recent regulatory filing. The company provides consulting services for business customers and specializes in developing software for statistical analysis, predictive modeling, and neural networks.

The filing indicates the capital is being raised in connection with a merger, acquisition, or exchange offer, but founding CEO Krishna Gopinathan did not respond to a call or e-mail seeking further information. According to the Global Analytics website, Gopinathan was the primary inventor of Falcon Fraud Manager, a neural-network technology developed at San Diego-based HNC Software (now part of Fair Isaac) that is used to protect most credit cards worldwide.

Global Analytics has been operating at least five years and has more than 100 employees, according to its website. A number of key executives at Global Analytics, including the executive vice president of analytics, vice president of products, and vice president of software development, are former HNC employees.

Last year, Global Analytics named Larry Rosenberger, the former CEO of Minneapolis, MN-based Fair Isaac, to its board of directors. The company also noted that Rosenberger and his wife Diane invested in the San Diego startup. Peter Rip, a general partner at San Francisco’s Crosslink Capital, also is on Global Analytics’ board, although Crosslink does not identify Global Analytics as a portfolio company.

Global Analytics also has formed a strategic partnership with Hewitt Associates, the Illinois-based human resources and outsourcing firm, and has been working on what it calls “the objective quantification of the value of human capital investments.” The company says it has been working with Hewitt in recent years to pioneer development of comprehensive models that tie such human resources metrics as talent attraction, retention, and engagement to shareholder value, creating what Hewitt calls its Human Capital Foresight.

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San Diego serial entrepreneur Michael Robertson is going to have to find something else to do now that Gizmo5, the VoIP (voice-over-Internet-protocol) company he founded in 2003, has become part of a certain search giant to the north. We have that news and more.

—Google confirmed that it’s buying San Diego-based Gizmo5, a six-year-old company that provides Internet-based calling software for mobile phones and computers. The service will become part of the Google Voice number-unification service. Google did not disclose the purchase price, which media reports put at about $30 million. Gizmo5’s 6 million users will still be able to use the service, according to a statement. But Google is suspending new Gizmo5 signups, and existing users can no longer sign up for a call-in number.

—Platformic, a Web-based startup that enables customers to create and manage their own websites, said it is adding social media capabilities. The two-year-old San Diego-based company, which has targeted broadcast companies, says its expanded software-as-a-service product will help a broadcaster’s audience share photos, create their own user profiles, and create personal blogs on the broadcaster’s Platformic-powered website.

—Qualcomm’s No. 2 executive opened a regional mobile technology conference in San Diego by providing an overview of steps the chipmaking giant is taking to help ease the pressure on wireless network bottlenecks as mobile data traffic soars. Qualcomm (NASDAQ: QCOM) Chief Operating Officer Len Lauer told the 3G CDMA Americas Regional Conference that in the year 2014, worldwide mobile data traffic in one month will exceed mobile data traffic for all of 2008.

—Technology innovations that help companies optimize their profitability will likely lead to the next wave of analytics-based software startups, according to Stephen Coggeshall of San Diego-based ID Analytics. Another hot area will be analytics that can help forecast consumer behavior, said Coggeshall, who was participating in a discussion about new opportunities in analytics during the San Diego Software Industry Council’s annual forum on analytics.

—Israel’s Panoramic Power won $250,000 and became the first winner of the top QPrize, the incentive prize competition launched earlier this year by Qualcomm Ventures. Panoramic Power is developing energy-monitoring wireless technology that enables a company or institution to deploy so-called “smart grid” technologies within their existing facilities.

—The San Diego-based Cannon Power Group said is getting $19.4 million in federal renewable energy grants to help fund construction of a giant wind farm in eastern Washington state, about 110 miles east of Portland, OR. The $1 billion Windy Point/Windy Flats project is expected to generate enough electricity for 250,000 homes.

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When Tom Clancy introduced a panel discussion yesterday at a forum on analytics software, the founder of San Diego’s Tao Venture Partners said the forum was “founded four years ago by people who had an interest in seeing San Diego get established as a leading cluster in the analytics space.”

The forum, which is sponsored by the San Diego Software Industry Council, offers an annual snapshot of local developments in a booming industry that has become crucial to business intelligence, data storage and management, and complex decision-making.

Since Robert Hecht-Nielsen founded HNC Software here in 1986, the number of companies that focus on analytics software in San Diego has mushroomed, with more than 100 companies specializing in neural networking, data mining, pattern recognition, and related algorithms and technologies for analyzing data. Yet Clancy and local experts who discussed “opportunities in analytics” lamented that San Diego’s standing as the birthplace of some key companies and technologies has gone largely unrecognized. Among the examples cited:

— HNC, which specialized in technology to analyze credit card transactions, was acquired for $810 million in 2002 by Fair Isaac and Co. and integrated with the Minneapolis, MN-company’s credit-scoring business.

—Urchin Software, a suburban San Diego Web analytics company that developed an assortment of tools for measuring website usage, page views, and other statistics, was acquired by Google in 2005 for an estimated $30 million. Seven months later, Google renamed its Urchin business Google Analytics, and made analytics tools available to Web users for free.

—WebSideStory, a San Diego company that developed website traffic analysis tools, rebranded itself as Visual Sciences in 2007 and was acquired later that same year for $394 million by Utah-based Omniture. (Last month, Omniture was itself acquired by San Jose, CA-based Adobe Systems in a $1.8 billion deal.)

—Carlsbad, CA-based analytics software developer Keylime Software was acquired for $9.5 million in 2003 by Pasadena, CA-based Overture, an advertising distribution network that was later acquired by Yahoo for $1.6 billion.

Such deals reflect a surging awareness of the value of data, says Stephen Coggeshall, a co-founder and chief technology officer for San Diego-based ID Analytics, which uses advanced analytics to search credit databases for telltale signs of identity theft. In terms of technology innovations that will likely lead to forming new companies, Coggeshall says …Next Page »

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San Diego-based Cyntellect , which makes work stations used by biotechs for cell analysis, purification, and processing, has raised $15.5 million so far in a secondary round that aims to raise a total of $18.6 million, according to a recent regulatory filing.

Cyntellect says its instruments are used in life sciences research, biopharmaceutical production, stem cell research, and drug discovery. The company says its cytometers provide scientists with rapid, high-quality imaging and analysis of cells in every well of a 384-well microplate array. Cyntellect says its instruments can scan an entire well while maintaining consistent illumination for accurate cell identification from the center to the well edge. The company’s product line also includes an automated system for cultivating cell lines used in biopharmaceutical manufacturing.

The current venture round consists of equity investments and convertible warrants, according to the filing. Cyntellect was founded in 1997, and earlier investors in the company include Bru II Venture Capital Fund, Iceland Genomics Ventures, Sigma-Aldrich, Sumitomo, and Third Security, according to VentureWire.

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Some San Diego life sciences companies reported a burst of new financing, while embattled Sequenom told investors it’s trying to conserve its available cash. Here’s our rundown of the latest highlights:

—San Diego’s Trius Therapeutics, a venture-backed biotech developing a new antibiotic for treating acute and life-threatening bacterial infections, disclosed plans to raise as much as $86 million in an initial public stock offering. With additional funding, the company will proceed to Phase 3 clinical trials of torezolid, which Trius describes as a second-generation successor to linezolid, the Pfizer antibiotic known as Zyvox.

—Life Technologies (NASDAQ: [[ticker: LIFE]]), the Carlsbad, CA-based provider of biotech instruments and lab supplies, agreed to acquire Woburn, MA-based BioTrove, which has developed a high throughput gene expression and genotyping analysis system.

— SpectraScience, the San Diego medical device maker, has raised more than $4.3 million through a private placement that combines preferred shares and warrants. SpectraScience (OTCBB: [[ticker: SCIE]]) CEO Jim Hitchin told Bruce the offering closes a $5 million round the company began earlier this year.

—PaxVax, a San Diego startup backed by Seattle’s Ignition Capital, has raised $2 million of a planned $6 million investment round. The biotech founded in early 2007 is developing a new type of vaccine that is administered as oral tablets and avoids much of the requirements that conventional vaccines require.

—Sequenom, San Diego’s embattled diagnostics company, said it expects to end the year with $39 million in cash—but that’s not enough to get through 2010 without raising funds or slowing spending. In April, Sequenom (NASDAQ: [[ticker: SQNM]]) disclosed that it had “mishandled data” from a prenatal Down syndrome diagnostic test, indefinitely postponing that product launch.

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San Diego-based Qualcomm (NASDAQ: QCOM) says Panoramic Power, a wireless sensor startup based in Kidron, Israel, is the winner of the first QPrize, the incentive prize competition launched earlier this year by Qualcomm Ventures. Panoramic Power has developed energy monitoring wireless technology that enables a company or institution to deploy Smart Grid technologies within their existing facilities. Panoramic Power, which previously won $100,000 as a QPrize regional winner, was awarded another $150,000 and the opportunity to compete in a global business plan competition held at the Mobile World Congress in Barcelona, Spain.

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The San Diego-based Cannon Power Group says it has received $19.4 million in federal renewable energy grants to help fund construction of a 400-megawatt wind farm in Klickitat County, WA, about 110 miles East of Portland, OR. Total investment in the project will be more than $1 billion. When completed, the Windy Point/Windy Flats project will be one of the largest wind farms in the nation, producing enough electricity for more than 250,000 homes per year. The project power has been designated for use by California municipalities.

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[Corrected 11/11/09, 3:15 pm. See below] Qualcomm chief operating officer, Len Lauer, says the San Diego wireless chipmaking giant is working across a broad front of technology development to accommodate a surge in wireless data traffic.

“The mobile Internet has arrived,” Lauer says in the opening keynote talk yesterday at the 2009 3G CDMA Americas Regional Conference. With more than 4 billion wireless subscribers around the world now—including 885 million 3G phone users—Lauer says the growth in wireless data is reflected by a roughly one-third increase in revenue reported over the past year by Verizon, AT&T, and other major carriers.

[Corrects to say Lauer was comparing monthly data traffic in 2014, not monthly growth in data traffic] By 2014, or just five years, Lauer says  worldwide mobile data traffic in one month will exceed total mobile data traffic for all of 2008.

Qualcomm founder and former chairman and CEO Irwin Jacobs and his son Paul Jacobs, who is Qualcomm’s current chairman and CEO, sounded a similar theme when they warned of capacity constraints last month during a keynote appearance at the CTIA Fall 2009 conference in San Diego.

In addition to the increasing demand for mobile data from smart phones and netbooks, Lauer says the trend can only accelerate as new wireless device categories proliferate, especially in what he calls machine-to-machine (M2M) communications. Examples of M2M technology developers include CardioNet, a Pennsylvania wireless health company that uses wireless sensors to continuously monitor heart patients for irregular heartbeats; wireless smart grid technologies being deployed by electric utilities (including San Diego Gas & Electric), and eBook devices like Amazon’s Kindle.

“Other operators are seeing this as a viable market, but it is going to take awhile to develop,” Lauer says, citing estimates that 229 million M2M cellular connections are forecast for 2013. “We do see from Qualcomm’s standpoint this being a very large opportunity for our chips.”

To cope with the surge in wireless data traffic, Lauer outlined a range of technology advances that Qualcomm has underway:

—The latest generation of advanced wireless receivers, which include updated revisions to the EV-DO (Evolution Data Optimized) telecommunications standard (part of Qualcomm’s CDMA2000 family), operate …Next Page »

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San Diego’s embattled Sequenom, which halted the debut of a new diagnostic product over mishandled data, is now considering steps to conserve cash. In an SEC document filed Monday, the life sciences tools company says it expects to end the year with $39 million in cash — too little to fund operations and capital expenditures at current levels through the end of 2010. There is “substantial doubt about our ability to continue as a going concern unless we adopt measures to conserve our cash and prolong our ability to operate,” Sequenom (NASDAQ: SQMN) says in its filing.

During a conference call, Sequenom’s interim CEO Harry Hixson said the company was in the process of developing a strategic and financial plan for 2010, and until the plan was completed, he could not estimate how long the $39 million would last. Last month, Sequenom named former Ligand Pharmaceuticals CFO Paul Meier as its interim CFO, effective today. Hixon says Sequenom also has put into place a cost control program to reduce unnecessary expenses and expects to reduce the number of programs it currently supports. He says some projects could be shelved, sold, out-licensed or partnered.

Bad news seems to keep coming from Sequenom, which stunned investors last April 29 with an announcement that the launch of the prenatal Down syndrome test would be delayed because scientific data had been mishandled. The company’s shares lost 76 percent of their value in trading the next day and have not recovered. The disclosure was a shock because just six days earlier – on April 23 – the company said the Down syndrome test was on track for a June launch. The SEC has opened an investigation to the company’s mishandling of its data and the Justice Department also is asking questions. The company has not fully explained what happened.

Hixson stepped in as interim CEO in September after the board fired former CEO Harry Stylli following an internal investigation. R&D senior vice president Elizabeth Dragon was also fired. CFO Paul Hawran resigned, as did another officer who was later revealed to be Steven Owings. Three employees also were terminated. Each has denied wrongdoing.

The company had previously said that none of the departing officers had benefitted from selling shares, but Hixson, who is also Sequenom’s chairman, said yesterday that in fact one of the officers had sold some stock to make a down payment on a house. The Wall Street Journal identified that officer as Owings, formerly the Sequenom vice president who oversaw development of prenatal diagnostics. Owings made nearly $300,000 from a series of stock sales on March 24. Hixson said the sales were “properly and timely reported” to the SEC. In addition, two lower-level employees who were terminated in September also sold stock, Hixson said.

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It was big news here in New England last week when Don Dodge announced on his blog that he had been laid off from Microsoft as part of some 800 layoffs at the software powerhouse. Dodge had been a regular on the innovation scene here in New England—and around the world, really—and was known as Microsoft’s enthusiastic ambassador to the startup world.

In his initial post about being laid off, Dodge, who was based in New England with the formal title of director of business development for the Emerging Business Team, said being laid off was “a total surprise” and that his bosses “offered no explanation.” But he kept his comments at a high level.

Since being laid off, Dodge has reported that he has picked up more than 1,500 Twitter followers. But other than that, I haven’t spotted much from him. That all changed today. Dodge not only posted (turns out he posted it yesterday, but I didn’t see it until today) a thoughtful piece on his blog about leaving Microsoft, he did a roughly 11-minute videotaped “exit interview” with TechCrunch.

To me, the more interesting of the two was Dodge’s own heartfelt post, called “Pay It Forward, give and you shall Receive.” He talks about the many friends, old and new, who reached out, the job offers the poured in, and more. Some excerpts:

“I want to publicly say thank you to all my friends. You know who your friends are when times are tough. I heard from hundreds of friends last week and it meant a lot to me. Social media has created a whole new set of “friends” who know a lot about you and care about you, even though you may have never met in person. Hundreds of these friends took the time to write to me. Over 400 emails on my new Gmail account. There were also hundreds of comments on blogs and news sites that carried the story of my separation from Microsoft. It was almost like I had died, but got to read my obituary and hear the tributes. It was surreal, uplifting, humbling, and very gratifying. Thank you. I had no idea…really.”

“Then of course there were the job offers or offers to discuss opportunities. They came from everywhere. The big tech companies, the biggest names in the business, were very quick to reach out, within hours of the news. I was pleasantly surprised. VC firms wanted to talk about opportunities at their firms and within their portfolio companies. Startup founders were also quick to act. Thank you all. I appreciate every single one of you.”

TechCrunch has done nothing to disguise its opinion of Microsoft’s decision; founder Michael Arrington, who conducted the “exit interview,” has called it a “huge mistake.” You can find TechCrunch’s post here. I’ve embedded the video below.

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