[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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Drug development programs got extended at two San Diego life sciences companies, while others had some good news on the fund-raising front. We wrap it all up for you here.

—Fate Therapeutics, a startup working to supply “industrialized” stem cells for the pharmaceutical industry without using embryos, said it raised $30 million in venture capital. That brings the total amount raised by the San Diego-based company to about $50 million since its inception two years ago.

—Cadence Pharmaceuticals (NASDAQ: CADX) said the FDA has delayed its review of the San Diego company’s intravenous pain reliever by three months, to Feb. 12. Cadence provided additional data to the FDA after an advisory panel raised concerns about liver damage from excessive doses of acetaminophen. But Cadence said it remains confident it will win FDA approval of its drug, which contains acetaminophen.

—Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) and its Big Pharma partner, Genzyme (NASDAQ: GENZ), have extended the timeline for their much-anticipated cholesterol-lowering drug by nearly a year. The companies reported encouraging results from a clinical trial, but noted that four out of 34 patients saw their liver enzymes increase to three times normal, a sign of potential liver damage. The companies plan to tinker with the dose of the injectible drug in future trials.

—San Diego-based NextImage Medical, a developer of a Web-based system for scheduling and managing diagnostic imaging services, reporting raising $5 million in a venture round led by Chrysalis Ventures of Louisville, KY.

—San Diego-based Altair Therapeutics, a company developing inhalable drugs to block inflammatory proteins involved in asthma and other respiratory diseases, has closed on the second part of a Series A venture financing, bringing the total amount raises this year to $17 million.

—San Diego-based Cyntellect, which makes work stations used by biotechs for cell analysis, purification, and processing, 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.

—GenVault, a Carlsbad, CA-based company that markets dry-storage technologies that allow scientists to store biological samples at room temperature, said it expects to break even by the end of next year. The startup has raised about $32 million so far.

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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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Early-stage tech financings are still chugging along, it seems. On the heels of yesterday’s news of a $5.25 million financing of Seattle stealth startup Doxo, I checked in with Keith McCall of Bellevue, WA-based Enroute Systems, a maker of parcel-shipping management software, to hear the latest on his company’s recent financing.

McCall, the company’s founder and CEO, says Enroute has closed an oversubscribed Series A round worth a total of $810,000. That includes more than $500,000 from Keiretsu Forum Northwest earlier this year, and a new investment (as of October) from W.R. “Ford” Smith, the founder of PetSmart. Other investors include Zino Society and Puget Sound Venture Club. (The Series A round also includes $60,000 that Enroute won in Zino Society’s investment forum this fall.)

Enroute makes a Web-based software platform that helps businesses choose the cheapest and fastest delivery service—international, national, or regional carriers—to ship their packages. McCall says the software reduces companies’ shipping costs by about 30 percent.

The startup has moved into new 4,500-square-foot digs in Bellevue—near the Burgermaster and Microsoft’s original offices—as of the start of November. It is now up to a dozen employees and has signed more than 50 business customers, including Zumiez, Natural Partners, Renton Western Wear, Theo Chocolate, BikeWagon.com, and Lumber Liquidators.

McCall, who previously founded Seattle-based e-mail and communications management firm Azaleos, says he expects Enroute to be profitable in the first half of next year, and is now focused on expanding its customer base.

With that in mind, he is already getting ready to raise more money. “For those investors who would like to join our existing angel investors today, we are immediately opening a $500K convertible note, which we anticipate converting to a Series B offering in 2010,” McCall says. He adds that the next formal capital raise “is targeted as a $3 million Series B.”

McCall says that next financing round will be focused on expanding the company’s shipping-management services to Asia and Europe. “We’re interested in continuing our momentum,” he says. “There’s huge opportunity for us to significantly reduce cost for businesses of all sizes.”

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Seattle-based Doxo, a stealthy tech startup, has raised $5.25 million in equity financing, according to a regulatory filing. The funding was reported by Northwest Innovation and TechFlash. The investors were not disclosed, but David Feinleib of Silicon Valley-based Mohr Davidow Ventures is listed on the SEC form as a director. Doxo was started by members of the “Qpass mafia” (former executives at Seattle-based Qpass), including Steve Shivers and Roger Parks.

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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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It was a busy week for local technology news.

—Two teams from San Diego and a third from Northern California demonstrated their development of advanced chemical sensor prototypes that are tiny enough to be found inside ordinary cell phones. The U.S. Department of Homeland Security is funding the Cell-All program, with a goal of basically creating an anti-terrorism app for cell phones that would enable authorities to crowd-source chemical detection.

—MaxLinear has filed for its initial public stock offering. The Carlsbad, CA-based fabless chipmaker, which specializes in designing semiconductor-based television receivers, intends to raise about $100 million through its IPO. The market may be de-frosting a bit, with 47 IPOs so far in 2009, compared with 45 last year, and 272 in 2007.

—ProQuo, a San Diego-based Web 2.0 company that was founded in 2007, was quietly shut down after taking in a total of $15 million in venture capital from Menlo Park, CA-based Draper Fisher Jurvetson and San Diego-based Mission Ventures. ProQuo was never able to validate its business model; its website offered consumers a way to remove their names from mass-mailing lists for free, and the company planned to sell its optimized lists back to mass marketing companies.

—San Diego’s wireless industry group, CommNexus, celebrated the opening of EvoNexus, its free high-tech incubator, by announcing the selection of three more startup companies: EcoATM, MicroPower Technologies, and TetraVue. CommNexus CEO Rory Moore says EvoNexus is believed to be the first incubator that is completely free for startups—that is, it doesn’t even require an equity stake in participating companies, as most incubuators do.

—Jitterbug, the San Diego wireless provider that puts an emphasis on simplicity, has acquired MobiWatch, a Waltham, MA-based startup developing mobile personal emergency response services. A regulatory filing shows that Jitterbug’s parent, GreatCall, provided 630,000 shares of common stock to MobiWatch and its shareholders in a deal valued at $107,100.

—San Diego-based Networkfleet is using its technology to help companies that operate fleets of vehicles go green by monitoring engine emissions and ensuring that vehicles are operating efficiently. Co-founder Diego Borrego told me the company also expects to be a player as consolidations sweep through the fleet tracking industry.

—EcoDog, a Vista, CA, cleantech startup that has developed a device that helps homeowners sniff out savings in their electric utility bill, was named best of show at GadgetFest, the annual fall competition sponsored by CommNexus, the San Diego wireless industry group. EcoDog founding CEO Ron Pitt won over the crowd when he declared, “My product is the only product up here tonight that saves you more money than it costs.”

—San Diego-based cleantech startup EESG is looking to raise $1.2 million to expand the 10-employee company’s sales staff, purchase inventory, and ramp up public relations and marketing. The company’s founders told me they have raised about half so far, including $300,000 from Longboard Capital Advisors, a green investment firm based in Santa Monica, CA.

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MaxLinear, a fabless RF chipmaker based in Carlsbad, CA, filed a registration statement today for an initial public stock offering, marking only the second IPO in the San Diego area since Bridgepoint Education made its debut on the New York Stock Exchange in April. About 45 IPOs have taken place nationwide so far this year.

Eight semiconductor industry veterans founded MaxLinear in 2003. The company specializes in designing highly integrated, CMOS (Complementary metal–oxide–semiconductor) chips, and has had notable success designing semiconductor-based TV tuners. Maxlinear says its customers include wireless module makers, original equipment manufacturers and original design manufacturers.

David Rodewald, an outside spokesman for the company, said MaxLinear executives would not comment beyond the statement issued today.

The number of shares to be offered and the price range for the offering were not disclosed, although Dow Jones says the Carlsbad company plans to sell an estimated $100 million in stock. The company plans to use the proceeds for working capital and general corporate purposes.

The founders self-funded MaxLinear for the first year, and co-founder and CEO Kishore Seendripu talked about their efforts to generate revenue by taking on consulting work and other outside work during a panel discussion on bootstrapping in San Diego six months ago. Seendripu defined bootstrapping as “a self-sustaining process that proceeds without external help.”

MaxLinear secured its first round of venture funding in late 2004, after completing development of its first prototype silicon television tuner using CMOS technology. The company identifies its venture investors on its website as San Diego-based Mission Ventures, U.S. Venture Partners of Menlo Park, CA, and Battery Ventures, which has offices in Waltham, MA, and Menlo Park, CA.

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Dave Paton and Dave Moody tell me they founded EESG, a San Diego cleantech startup also known as Energy Efficiency Systems Group, last year in anticipation that soaring energy prices would unleash strong demand for practical alternatives. But they didn’t focus on new technologies for alternative energy sources. They focused on energy efficiencies.

They also wanted to take advantage of their extensive experience with the hotel industry. Paton had spent 30 years working as an executive at the Hilton, Radisson, and Doubletree hotel companies. And the company the pair had previously founded, Vista, CA-based Paramount International Telecom, provided a voice-activated automated attendant and message system for the hospitality industry. So they knew hotels. As Paton and Moody put it, they understood that for a hotel to keep its four-star rating, it was going to have to keep the air-conditioning running through the summer.

As a result, Paton and Moody concluded that developing technologies to help hotels and other facilities improve their energy efficiency was a likely growth business ideally suited to their expertise and industry contacts. And it was a business that wouldn’t require huge amounts of external capital. The business partners say they set out to create a system that incorporated the best technologies for sensing and measuring energy use, for monitoring and communicating such information in meaningful ways, and for remotely managing everything—from the 15-ton air-conditioning chiller on the roof to the boiler in the basement.

“Every piece of equipment has a sweet spot that it operates at with optimum efficiency,” Moody says. The energy conservation and management systems that EESG has developed are designed to identify equipment throughout a facility, and to optimize the performance of each unit. “We know every model, every unit, every product type, and we know how to control it,” Moody says. “Our system is specifically programmed for that equipment, say a Trane 360, and to keep it operating at that sweet spot.”

To tie it all together, they hired software engineers to develop proprietary software analytics that provide a comprehensive and real-time energy audit of customer facilities. EESG also developed a Web-based interface that can be accessed online or by a smart phone. Paton says their system, once installed, reduces customers’ energy consumption by 8 percent to 15 percent annually. The partners say EESG has implemented its technology so far at four hotels in the U.S. and Canada, including the luxury Fairmont Hotel in Washington D.C.

Fairmont Hotel

“The building engineer can be anywhere in the world,” Moody says. “You just go to a secure portal, and see how the system is operating. Or maybe the vice president of asset management wants to drill down to one chiller at one property, but he also wants it aggregated to show all the chillers at all the buildings that he manages.”

So far, the founders have funded EESG’s technology development themselves, along with friends and family. But they are now looking to raise about $1.2 million to expand the 10-employee company’s sales staff, purchase inventory, and for public relations and marketing.

Moody and Paton say they have raised about half from wealthy individual investors and cleantech investment funds, such as Longboard Capital Advisors of Santa Monica, CA, which has invested $300,000 from its Blue Earth Fund in EESG’s current round.

“Although we typically do not invest in early stage companies, it was an easy choice to invest in the management at rapidly growing EESG,” Longboard managing partner Brett Conrad wrote in an e-mail to me last night. “We felt like our investment risk was further reduced by management’s deep experience and relationships in hotel and resort management around the world. Because Longboard Capital Advisors focuses on clean tech investing, we are particularly excited by EESG reducing their customer’s carbon output while at the same time while achieving extraordinary ROI’s by significantly reducing energy costs from power hungry air conditioners, elevators and escalators.”

Moody sums it up a little more succinctly. “It is a good green thing for sure,” he says, “but the bottom line is that it helps you save money.”

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TEDMED had Martha, Goldie, and other celebrity speakers, but San Diego-based Amylin Pharmaceuticals broke this week’s big news when it signed up a big Japanese partner to develop its line of obesity drugs. It’s all part of your regular dose of San Diego biotech news, and it’s ready now:

—Amylin Pharmaceuticals, the San Diego-based diabetes drug specialist, announced that it has formed a partnership with Japan’s Takeda Pharmaceuticals, which agreed to carry most of the development costs for Amylin’s weight-loss drugs. In return, Takeda gets a worldwide exclusive license to eventually commercialize Amylin’s experimental obesity drugs, including the combination of pramlintide and metreleptin, and davalintide.

—After a five-year hiatus, TEDMED founder Richard Saul Wurman, and president, Marc Hodosh (who also is an Xconomist), brought the conference on medical technology, entertainment and design to San Diego’s Hotel del Coronado. TEDMED announced during the conference, which included presentations by Boston Scientific co-founder (and Xconomist) John Abele, Martha Stewart, and Goldie Hawn, that the conference will return to the same location next October.

—I only had time to attend a fraction of the presentations at TEDMED last week. One of my favorites talks, though, was delivered by Bill Davenhall, who leads the health and human services marketing team at ESRI, the Redlands, CA, giant in geographic information systems. Davenhall talked about the importance of including patients’ “place histories” as part of their medical records and raised an interesting question: Will the electronic health record systems being created today have the capability to add data in new categories—such as “geo-medicine”–that aren’t typically included in today’s patient records?

—New York-based Xenomics filed a lawsuit against San Diego-based Sequenom that alleges Sequenom misrepresented the progress in its development of a prenatal test for Downs syndrome. Xenomix says it would not have licensed its patents to Sequenom had it known the truth.

—Denise profiled San Diego-based Sirigen, an early stage medical diagnostic company that is developing technology that uses light-emitting polymers to detect bits of DNA. Sirigen founder Brent Gaylord developed the technology at UC Santa Barbara, extending the significance of UCSB physicist and Nobel laureate Alan Heeger’s discovery of conductive polymers.

—The FDA told San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) and its partner Eli Lilly the companies can now market exenatide (Byetta) as a frontline, standalone therapy for diabetes. The drug was previously approved for use with other drugs, or as a fallback option when other tretments failed.

—Vertex (NASDAQ: VRTX), the Cambridge, MA, biotech with operations in San Diego, said the latest trial of its telaprevir treatment for hepatitis C was able to attain the clinical definition of a cure in more than 80 percent of patients who got the drug. The finding is part of the mounting evidence Vertex is gathering on its quest to develop the first-of-its-kind protease inhibitor for the chronic liver disease.

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EvoNexus, San Diego’s free high-tech incubator, announced that it has enrolled three more startup companies during ceremonies yesterday that officially marked the opening of its new facility.

CommNexus, the San Diego wireless industry group, announced five months ago that it was leading the creation of the free and “no strings attached” startup incubator, to be headed by wireless industry executive Cathy Pucher. EvoNexus, which is structured as a nonprofit organization, plans to eventually house 10 to 12 technology startups; it named its first three startups less than two months ago.

CommNexus and EvoNexus have both moved their offices into part of a 25,000-square-foot commercial office building that was previously occupied by San Diego-based Leap Wireless, (NASDAQ: LEAP), which sells prepaid discount mobile phone service through its Cricket Communications subsidiary. By providing the office space to EvoNexus for one year at no cost, Leap made the largest single contribution of more than three dozen companies and individuals that donated in-kind services and cash to the incubator, according to Pucher.

“San Diego is an innovation economy,” Leap CEO S. Douglas Hutcheson told the crowd. “We’ve spawned more new companies in San Diego than I think anyone would have believed, and it’s vital that we support that.”

For the startups that are lucky enough to get selected, the incubator provides free office space, including utilities, Internet service, office equipment, and volunteer business mentoring for up to two years.

“Other cities don’t recognize the collaboration that we have here,” San Diego Mayor Jerry Sanders told a lunchtime crowd of roughly 150 people who attended a ribbon-cutting ceremony for the incubator. The mayor was joined by other local dignitaries and industry officials, including CommNexus board chairman John Major, the former chairman and CEO of two San Diego wireless companies, Novatel Wireless and Wireless Knowledge. “As we entered into the recession of recessions, a lot of non-profits hunkered down, and frankly that would have been the easy thing for us as well,” Major said. “But that’s not the way we operate.”

Pucher, the incubator’s executive director, told me …Next Page »

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It was a quiet week for deals in the Northwest, but we dug up some important ones in business software, wireless, and biotech.

—Seattle-based Amazon’s (NASDAQ: AMZN) acquisition of Zappos, the online apparel and shoe seller based in Las Vegas, has closed. The deal, first announced back in July, is valued at $1.2 billion in Amazon stock.

—Bellevue, WA-based Onehub has raised $1.3 million in Series A funding from Ignition Partners and angel investors. The company was founded in 2007 and makes Web-based software for business collaboration and file-sharing.

—We took a close look at small financing deals in the Northwest, worth between $100,000 and $1 million, that have flown under most people’s radar in the past month. According to stats from ChubbyBrain, a New York-based information and data services company tracking the innovation economy, the following companies raised a small amount of equity in September: Acucela, Adometry, BallLogic, InEnTec, Inson Medical Systems, Second Porch, Site 9, SynapticMash, Smilebox, Vantos, and WA 32609.

—Seattle-based Kineta, a biotech firm developing drugs to fight autoimmune diseases, has formed a strategic alliance with MPI Research, based in Michigan, as Luke reported. Financial terms of the deal weren’t given, but Kineta said it will receive support for animal studies that will enable the company to begin clinical trials next year.

—Portland, OR-based RF Arrays raised $6.5 million in equity, options, warrants, and/or other rights to acquire securities, according to a regulatory filing. The investors were not disclosed, but New York-based New Science Ventures has previously backed RF Arrays, which develops wireless communications technology.

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San Diego’s tech sector got some money and glory during a week that was overshadowed by news from two life science conferences: TEDMED and the annual Biocom Investor Conference. Get your tech news now while it’s still hot.

—To stay connected with open-source development for smart phones, San Diego’s Qualcomm created a subsidiary, the Qualcomm Innovation Center, that is focused on making sure the chipmaker’s technology works smoothly with Android, Symbian, and other open-source wireless platforms. Qualcomm (NASDAQ: QCOM) also joined the Symbian Foundation and is supporting the open source systems used by Nokia and others.

—One of the big selling points for algae-based fuels is that algae absorbs a lot of carbon dioxide before it gets harvested and turned into biofuels. Yet San Diego-based Sapphire Energy and other algae biofuel companies say they are having a hard time getting enough carbon dioxide at an affordable price to support their research and development efforts.

—Federal stimulus funds will help cover almost half the cost of a new $60 million wireless communications system that San Diego Gas & Electric is developing as part of its smart grid program. The $28.1 million grant is part of $3.4 billion to be allocated nationwide.

—Carlsbad CA-based Verdezyne, which is applying advanced biotechnology tools to the development of industrial chemicals and biofuels, raised nearly $3 million of a planned $15.2 million round of venture capital.

—JMI Equity, the venture firm based in San Diego and Baltimore, led a $5 million investment in Axeda, the Waltham, MA-based startup that makes a cloud-based system for wireless tracking of company assets. Axeda also raised $4 million in venture debt from MMV Financial of Toronto.

—TechAmerica San Diego, the local chapter of the industry group previously known as the AeA, issued nine awards at its 16th annual high tech awards luncheon. The group named winners in nine categories: MadCap Software (Software); InterKnowlogy (Internet); Verari Systems (Hardware); Quake Global (Communications); SeaBotix Inc. (Defense); Peregrine Semiconductor (Integrated Circuits); OneRecovery (Medical Device) IPS Group (Cleantech); Legend Films (Emerging Growth).

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Carlsbad CA-based Verdezyne, which just disclosed a $1.7 million government grant, has raised nearly $3 million of a planned $15.2 million round of venture capital, according to a regulatory filing yesterday.

The company, which was previously known as CODA Genomics, is developing genetic engineering techniques and processes for producing industrial chemicals and fuels from microbes. When Verdezyne announced two weeks ago it had received the $1.7 million Small Business Technology Transfer grant, the company said the funds would be used to develop gene libraries for its computational and bioinformatics programs.

Details about Verdezyne’s latest venture round are not available, as CEO William Radany is out of the country. In an interview four months ago, Verezyne’s vice president of business development, Damien Perriman, said the company is directing its activities at both improved ethanol fermentation and new ways of producing chemicals. Perriman said the company’s technology could help ethanol producers now sitting idle by improving yields, reducing carbon dioxide emissions, and speeding up the ethanol fermentation process.

Verdezyne’s existing investors include Monitor Ventures, which has offices in Los Angeles and Palo Alto, CA, Seattle-based OVP Venture Partners, Southern California’s Tech Coast Angels, and the Life Science Angels. While the company does not list San Diego’s Enterprise Partners Venture Capital as an investor, managing director Drew Senyei sits on the company’s board of directors.

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They are the deals that slip through the cracks unnoticed. They are worth less than $1 million, but at least $100,000. Though small in size, these investments need to be included along with the bigger deals that get more press, if you want a more complete picture of the funding landscape in the innovation community. And there were at least 16 of these deals in the Northwest in September (see table below), according to ChubbyBrain, a New York-based information services company tracking VC, angel, and other investments in private companies.

It’s probably too soon to talk about trends, because this is the first month we’ve had access to ChubbyBrain’s data on these smaller deals, which were compiled from regulatory filings, user submissions, and other sources. But here are some quick observations.

About two-thirds of the deals (11 of 16) were equity investments, while one-third (5 of 16) were debt financings. Half the investments (8) were in software companies, while about a quarter each were in biotech/medical (4) and cleantech (3) firms. The majority of the deals were in the Seattle area (10), but a significant number were near Portland or in Oregon (6). Anecdotally, all those breakdowns seem consistent with the deal flow we’ve been seeing and reporting on in the Northwest for the past year or so. The data didn’t include the investors or the stage of the investments.

Without further ado, here are the 16 “under the radar” deals from last month:

Vantos (Seattle)                                            Equity        $873,487
Investigation software

InEnTec (Bend, OR)                                     Equity        $800,000
Cleantech fuels

WA 32609 (Redmond, WA)                           Equity         $800,000
Biotech

Inson Medical Systems (Bellevue, WA)      Equity         $642,536
Biomedical drug delivery

Napera Networks (Mercer Island, WA)         Debt           $600,000
Networking software

Acucela (Bothell, WA)                                    Equity         $439,603
Biotech drugs

Adometry (Kirkland, WA)                               Equity         $400,000
Analytics software

Smilebox (Redmond, WA)                              Equity         $399,999
Consumer software

Asemblon (Redmond, WA)                             Debt            $386,000
Cleantech/materials

Ohio River Clean Fuels / Baard Energy (Vancouver, WA)    Debt            $245,000
Cleantech fuels

Safetec Compliance Systems (Vancouver, WA)                    Debt            $235,000
Software for chemical compliance

Second Porch (Portland, OR)                          Equity         $225,000
Social software

SynapticMash (Seattle)                                    Equity         $200,000
Educational software

Silere Medical Technology (Kirkland, WA)      Debt            $120,000
Medical devices

BallLogic (Portland, OR)                                   Equity         $100,000
Consumer devices

Site 9 (Portland, OR)                                          Equity         $100,000
Web development software

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[Updated 10/27/09 12:55 pm. See below.] The Department of Energy has released a list of utilities that are getting federal grants to spur energy innovations under the $787 billion economic stimulus package, and San Diego Gas & Electric is getting $28.1 million to help build out its “smart grid” system.

Additional details are expected to follow President Obama’s speech at a solar facility in Florida, where he is expected to announce grants totaling $3.4 billion—the largest award made under the stimulus package in one day. The grants, which range from $400,000 to $200 million, are intended to help utilities build smart grid systems (which help consumers save money by providing real-time monitoring of their energy use), upgrade local power grids to reduce blackouts, and boost use of renewable energy.

The $3.4 billion is being allotted through 100 government grants in 49 states that will be matched by $4.7 billion in private investments.

[Updates below with new information from SDG&E and clarifies that the utility formed the coalition as part of a second grant application] SDG&E, a utility operated by San Diego’s Sempra Energy, said in September it has formed a coalition with the non-profit group Cleantech San Diego, UC San Diego, and major companies like Qualcomm, IBM, Cisco, and Intel. The coalitions was formed as part of a separate grant application that seeks $100 million for a regional demonstration system to help SDG&E manage the increasing demands on its power grid from electric vehicles as well as fluctuations in energy supplied to the grid by wind, solar and other renewable energy sources.

“It’s all part of the broader smart grid funding that the federal government has put aside,” says Chris Baker, a senior vice president for shared services and chief information officer for SDG&E and its sister utility, Southern California Gas. “You can’t do a smart grid without an enabling communications infrastructure.”

Baker says the $28.1 million DOE grant will enable the San Diego utility to address a variety of wireless communications needs with a more comprehensive plan. For example, while the utility has installed about 130,000 smart meters so far, Baker says the grant will enable SDG&E to establish a dedicated 700 megahertz “takeout point” for transmitting data from the smart meters’ wireless mesh network. The $28.1 million grant to SDG&E from the DOE will cover almost half of the $60 million project. The funding also enables the utility to install high-bandwidth wireless capabilities at its substations and certain corners of its grid.

SDG&E is working to integrate 1.4 million wireless “smart meters,” which the utility has been installing, with an advanced IT system that will allow increased monitoring, communication, and control of a regional power grid that spans 4,100 square miles.

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Much of last week’s San Diego business news involved venture capital—how much VC cash was recently invested in this area, and how the local tech community is working to get more. Read on, gentle reader, for all the VC wranglings and the rest of the biz tech happenings:

—The decline in San Diego-based venture capital firms prompted the technology community to form a task force to increase the access to capital for early-stage companies here. Windward Ventures’ managing partner Dave Titus is leading the task force. He told me, “When you’re talking about early stage companies, they don’t get done by out-of-town venture capital firms. They just don’t.”

—V-Vehicle, the San Diego-based startup car manufacturer, was the single biggest recipient of venture capital—raising $62.25 million—during the three months that ended Sept. 30, according to data from Dow Jones VentureSource. It was among 29 startups that got a total of $248 million in venture dollars during the third quarter.

—During a panel discussion organized by the San Diego Venture Group, Mission Venture’s Leo Spiegel says his VC firm has been meeting with institutional investors with the intent of raising money for another venture fund. “We’d like to see more innovation in San Diego,” Spiegel said.

—In a presentation at San Diego’s MIT Enterprise Forum, MojoPages founder and CEO Jon Carder sought advice on how to build its online community and take advantage of its access to free advertising as the San Diego Internet startup expands. Carder said the company’s core business combines a searchable online business directory with a social network that provides consumer reviews of local merchants, restaurants, service providers, and other businesses. Carder views Yelp as their biggest competitor.

—The Founder Institute, which provides training courses for startup CEOs, is finalizing enrollment for its inaugural San Diego class. The business mentoring program, which meets weekly over a four-month period, began in San Francisco earlier this year and is expanding to San Diego and other cities over the next few months.

—Brendan Boyd and partners Jan Anton and Eric Jacobson have re-branded their e-commerce website previously known as iSelfStore.com and launched it as Onemarketplace.com. The company’s Web-based application enables people to fill out a single form to sell items simultaneously on eBay, Amazon, Craigslist, and other merchandise sites.

—San Diego-based Senomyx (NASDAQ: SNMX) says it can now begin commercializing S6973, a compound it has developed to intensify the sweetness of sugar. The compound could help food makers reduce the amount of sugar they put into prepared foods.

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A breakfast discussion on “Getting Ready for the Rebound” held yesterday by the San Diego Venture Group might have been more aptly billed as “Waiting for the Rebound: A Tragicomedy in Two Acts.” But then again, with San Diego News Network CEO Neil Senturia serving as moderator, there really can only be one act.

The irrepressible Senturia was in his element (which is to say he was on stage) as he delivered one-liners while leading a panel of local experts through a conversation about the rebound that ranged from the venture capital outlook in San Diego to Wall Street ethics and the overall U.S. economy.

So, for example, as UC San Diego Economist Allan Timmermann talked about government spending and the prospects of inflation, Senturia interjected, “Inflation is what allows you to live in a more expensive neighborhood without moving.” And when Mission Ventures managing partner Leo Spiegel talked about the strength of character he looks for in startup entrepreneurs, saying, “I want to see that they went to the wall,” Senturia quipped, “You mean the wailing wall.”

As the only economist on the panel, Timmermann was an obvious target for such Senturian gibes as, “If you put 10 economists in a room, you get 11 opinions.” But a riposte from the UCSD economist got one of the biggest laughs when Senturia indignantly denounced the outrageous pay and bonus demands of disgraced Wall Street executives, the corruption of Bernie Madoff, the alleged corruption of hedge fund manager Raj Rajaratnam—and demanded the panelists explain what has happened to American ethics. Timmermann answered, “It’s only when the tide retreats that you see who’s swimming naked.” The audience roared.

But seriously folks, the conversation about preparing for a rebound led to a number of interesting points and observations:

—The outlook for venture-backed companies is clearly improving, according to Mission Ventures’ Spiegel. Following what he describes as a “brutal” period last winter, in which a third of the employees were laid off across Mission Ventures’ 30 portfolio companies, Spiegel says two of those ventures are now responding to buyout offers and a third is …Next Page »

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