New England drug developers made headlines this week with funding news.

—My San Diego colleague Bruce took a look at Applied Proteomics, the five-year-old biotech startup co-founded by MIT-trained computer scientist Danny Hillis. The startup, which raised $22.5 million in funding in June, is developing technology that provides a 40-gigabyte snapshot of all the proteins circulating in a drop of blood.

—Radius Health, a Cambridge, MA-based startup developing treatments for osteoporosis, filed paperwork indicating its intent to raise $86 million in an initial public offering.

—Investing dollars in biotech and medical devices startups increased in 2011, but the volume of deals shrank, according to a report by PricewaterhouseCoopers and the National Venture Capital Association. Read more of my colleague Arlene’s recap.

—New Jersey-based Celgene (NASDAQ: CELG) continued its recent streak of deals with Boston biotechs, with a $15 million investment in Acetylon Pharmaceuticals, a startup funded by New England Patriots owner Robert Kraft. (That should be some consolation.)

—Waltham, MA-based Synchroneuron raised $6 million in funding from Morningside Technology Ventures—a milestone for founder Barry Fogel, who has been working for 15 years on a treatment for a movement disorder called tardive dyskinesia (TD).

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The United States is essentially an unpopulated wilderness. If you scattered the citizenry evenly across the country, we’d each have a luxurious eight acres to ourselves. But here’s the weird thing: In a country where the outdoors is so vast, people rarely go there. Even folks who think of themselves as outdoorsy types don’t leave the house much—only 24 percent of outdoor enthusiasts say they get outside two or more times per week, according to a 2010 study by the Outdoor Industry Association.

Why don’t more people hit the trails? The surprising reason, according to many studies, is that they don’t know where to go. And the Internet isn’t much help. Key information about hiking and cycling destinations—the locations of trailheads and the length and difficulty of each route, for example—is either fragmented across thousands of websites run by federal, state, or municipal agencies, or stuck behind paywalls. If you’re looking for a restaurant near a trailhead, Yelp will show you lots of options. But as for the trail itself, good luck.

That’s the gap a San Francisco startup called AllTrails is trying to fill. A 2010 graduate of the AngelPad startup accelerator program, the company offers an exhaustive online database of trails and trail reviews from hikers, as well as GPS-enabled iPhone and Android apps that help users plan, document, and share their outdoor adventures. More than 200,000 people have joined AllTrails so far, and its iPhone app persistently ranks among the iTune’s App Store’s top 100 free travel apps.

The AllTrails team

The company, which is backed by 2020 Ventures, Camp Ventures, and 500 Startups, also sends out a handy e-mail every Thursday with suggestions for weekend hiking or biking trips, customized to each user’s location and past preferences. I’ve followed up on AllTrails’ suggestions several times, and I haven’t been disappointed yet. My favorite AllTrails find: Berry Falls Loop, a 10.4-mile trail along a meandering creekbed adjacent to Big Basin State Park near Santa Cruz, CA.

All of this information is free. But next month, AllTrails plans to introduce a premium, subscription-based version of its service that will give users exclusive access to GPS route information for each trail, as well as topographical and illustrated maps from National Geographic. I visited AllTrails a couple of weeks ago to get the scoop on the new premium services from Russell Cook, the company’s founder.

The alliance with National Geographic, announced in January, is probably the biggest thing to happen to the six-employee startup since it got admitted to AngelPad, Cook says. It’s not just a content-sharing arrangement: the entire AllTrails site is now co-branded with National Geographic, and AllTrails is about to take over management of TOPO.com, a service of National Geographic that sells PDF versions of topographical maps. “If you had asked me back during AngelPad who we wanted to work with, there would be no one else even close to number one,” says Cook. “No one is better known for their spirit of adventure or their quality of information.”

I’ll say more on that partnership in a minute. But why did Cook think there was a need for a new outdoor-recreation site in the first place?

Well, if you’re like me and you spent a lot of time searching online for trail information, you’ve probably run into a site called Trails.com. A product of the first dot-com boom, Trails.com has built up one of the Web’s largest collections of online trail guides. (The site got sucked into the Demand Media empire in 2006 when Demand bought its parent company, Hillclimb Media.) The site’s pages score highly in Google’s search results, and if you’re looking for a good trail to hike in a given region, Trails.com will usually have … Next Page »

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Time for an update on Boston’s marketing tech cluster. It’s one of the real strengths of the local entrepreneurial ecosystem. And it looks like it’s getting stronger, with a couple of leaders making news this week. Here is a tale of two companies that have become competitors:

—Constant Contact (NASDAQ: CTCT), the Waltham, MA-based online marketing firm, has seen its stock price jump nearly 30 percent—from about $24 to just over $30—since Facebook filed for its IPO last week (coincidence?). Constant Contact has been positioning itself as a leader in digital marketing for small businesses across e-mail, social media, and Web platforms—especially social campaigns. The company also released some promising stats on its revenues and profits for 2011 and its most recent quarter.

—HubSpot, the Cambridge, MA-based marketing tech firm, said it has hired J.D. Sherman, Akamai’s former chief financial officer (also a former IBM exec). The company says Sherman is being brought in partly to help it prepare for a future IPO. HubSpot has been hiring aggressively and working on new products, while it pares away others (like Oneforty.com, which it acquired last summer). It remains to be seen whether the company will actually make it to an IPO before getting snapped up by Salesforce.com or some other suitor.

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Last month, Aastrom Biosciences president and CEO Tim Mayleben and his wife, Dawn, announced they are funding a new “venture shaping” program at the University of Michigan.

Venture shaping refers to the process of systematically vetting a nifty idea for a startup, with the idea that the failure of a less-than-viable business will occur at a much earlier stage before too much financial damage has been done—a key component in supporting new businesses led by student and faculty entrepreneurs.

“My wife and I decided we wanted to give back, and we liked [managing director of U-M's Zell Lurie Institute] Tim Faley’s scientific approach to new company creation,” Mayleben (see photo below) says.

What the Mayleben Family Venture Shaping Program will do, Mayleben says, is help students weed out failing business ideas earlier. Grants of $500 will be awarded to approximately 25 teams of students or faculty who have an idea for a startup that they want to test or refine. Each team will then evaluate their idea for profitability and market viability through a three-step process.

“The grant is meant to encourage students to do business discovery work,” Faley says. “People are writing plans on vague ideas. That’s an interesting first pass, but go talk to the potential customers and find out what the revenue stream might look like.”

Faley calls the venture shaping program a needed bridge between the university’s 1,000 Pitches competition, which generates raw ideas, and the Dare to Dream program, which awards up to $10,000 to the most promising of those ideas.

“To get students to do the [venture shaping] work without an incentive was challenging,” Faley says. “It fills in a really nice gap.”

Aastrom is an Ann Arbor, MI-based startup that recently entered the final stage of clinical trials for its multicell therapy for patients with critical limb isschemia. Mayleben has a lots of experience developing life sciences startups. Before joining Aastrom, he served as chief operating officer of Esperion Therapeutics, which raised more than $200 million in capital under his direction before being acquired by Pfizer in 2003.

Mayleben says he has gotten to know the folks at Zell Lurie by serving as both a formal and informal advisor to the student-managed Wolverine Venture Fund for the past decade. He likes the school’s disciplined approach to failing early. He says university entrepreneurial programs fall short when they only track the number of companies created.

“The more relevant score is how many successful businesses get launched,” Mayleben says. “The venture shaping program will increase the likelihood of success, and that’s especially true for first-time entrepreneurs.”

Faley says he and the university are thrilled that the Maylebens are funding the program, and he says they’ve already expressed that they’ll entertain the idea of providing more venture shaping grants if the program grows the way Faley hopes that it will.

“Tim is a very successful serial entrepreneur, but he’s also a very thoughtful and methodical person,” Faley says of Mayleben. “That helps us when we’re trying to move students through the program.”

The first recipients of the Mayleben Family Venture Shaping Program will be announced on February 17 during the Michigan Business Challenge finals.

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When Barry Fogel first started developing a new treatment 15 years ago, his main goal was to help his own patients. Fogel, a physician trained in both psychiatry and neurology, saw many patients with a movement disorder called tardive dyskinesia (TD). The condition—which can be caused by drugs that block dopamine, such as antipsychotics—is characterized by involuntary movements of the face like puckering, closed eyes, and grimacing. Some patients suffer writhing of their hands and feet, or difficulty moving their upper bodies. “At its worst, it’s quite disfiguring,” Fogel says. And there is no approved drug to treat TD.

Fogel developed a treatment for the condition in the late 1990s, patented it, and set out to try to get it on the market. On Monday, Fogel’s dream took a huge leap towards reality when his Waltham, MA-based company, Synchroneuron, announced it had raised its first round of venture capital—$6 million from Morningside Technology Ventures. It’s enough to take the drug through a substantial portion of the clinical trials Synchroneuron will need to complete to apply for FDA approval, says chief financial officer Marc Cote.

Synchroneuron’s journey from idea to Series A could be a case study in stick-to-it-tiveness—and the value of networking. Fogel, a clinical professor of psychiatry at Harvard Medical School, suspected that modulating two brain chemicals, glutamate and GABA, would relieve TD. So he did a bit of experimenting on his own patients, prescribing them existing drugs that targeted those chemicals but were approved to treat other conditions. “I established that if you modulate glutamate, in particular, the TD gets better,” Fogel says.

So Fogel developed and patented a method for using a drug called acamprosate to do just that, and in 2004, he licensed it to San Diego-based Somaxon Pharmaceuticals (NASDAQ: SOMX). But Somaxon was developing an insomnia drug, which took precedence over the acamprosate program, Fogel says. “They didn’t give sufficient resources to acamprosate,” he says. “The progress was disappointing.” Somaxon declined to comment. (A sidenote: Somaxon eventually did get its insomnia drug on the market, but has struggled to make it stand out in a competitive market.)

In 2007, Fogel got his patents back from Somaxon and began looking for an alternate path to FDA approval. It wasn’t easy: Fogel and his wife had to do all the work to … Next Page »

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Today’s West Coast announcement that Oracle is buying human resources management firm Taleo for $1.9 billion—yes, billion—puts some Boston-area talent and recruiting startups in a new light. Unfortunately, one of them is no longer in Boston…

—Take the Interview, the video-based recruiting startup and former Dogpatch Labs Cambridge resident, has relocated to New York City (SoHo to be more exact). It’s not a big surprise, as the company was part of the DreamIt Ventures startup program in New York last summer. Take the Interview, led by CEO Danielle Weinblatt, raised a seed funding round last September.

—Boston-based Smarterer, a skills-test startup that’s trying to reinvent the resume, has hit a possible inflection point. According to co-founder Dave Balter, the company had 800,000 skills questions answered online over the past year, but recently that figure increased by 250,000 in just five days. Chalk it up to focusing on who wants to use the product and then who has to use the product (employers vs. job seekers). Smarterer is led by CEO Jennifer Fremont-Smith; the company raised a seed round last year.

—Senexx, an expertise-management startup based in Cambridge, MA, and Israel, has collaborated with fellow Cambridge startup PowerInbox to build a Web application that runs in people’s e-mail systems and helps them find expertise and share knowledge within their company or organization. This is an interesting partnership between a couple of early-stage startups trying to do big things in social enterprise apps, using e-mail as the platform.

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New England Patriots owner Robert Kraft may still be smarting from his team’s loss to the New York Giants in the Super Bowl, but at least one of Kraft’s other organizations has some good news to cushion the blow: Boston-based Acetylon said today that it has received a $15 million equity investment from Celgene (NASDAQ: CELG), the biotech giant based in Summit, NJ.

Acetylon was founded in 2008 and backed with $40 million from several individual investors, including Kraft. The company is working on a class of drugs that inhibit enzymes called histone deacetylases (HDACs). These enzymes regulate gene expression and play a role in many cancers. Last fall, Acetylon began human trials of its lead compound, ACY-1215, in multiple myeloma. Celgene is a leader in that field with its blockbuster myeloma treatment lenalidomide (Revlimid). “Celgene has a strong strategic and market interest in hematological malignancies and other cancers, and we will benefit from their guidance and input,” says Walter Ogier, CEO of Acetylon.

In the past, drug developers have tried to inhibit several HDACs at one time, but Acetylon’s compound targets only one, HDAC6. That selectivity may cut down on side effects such as fatigue and nausea—and it was one of the main reasons Celgene was attracted to Acetylon’s research. “Acetylon has established itself as the leader in developing next generation, selective HDAC inhibitors for cancers as well as non-cancer disease indications and we believe the company’s approach could significantly benefit patients,” said Mark Alles, Celgene’s chief commercial officer, in today’s release.

Acetylon’s scientists plan to test ACY-1215 in combination with bortezomib (Velcade), made by Millennium Pharmaceuticals. “We anticipate a similar opportunity to test it in combination with [Celgene's lenalidomide] and potentially the next-generation of the drug,” which Celgene is currently testing in clinical trials, Ogier says.

Celgene’s investment in Acetylon is a pure equity deal, and Celgene will not receive rights or options to the startup’s technology. Alles will take a position on Acetylon’s board as a non-voting observer—meaning he’ll mostly have an advisory role. “They’ll have a closer view on our progress,” Ogier says. As for whether or not Celgene might become interested in forming a closer research alliance in the future, Ogier says, “anything could happen.” In the meantime, the deal “doesn’t preclude us from forming other partnerships,” he says. “I think this is good for both companies.”

Celgene has taken quite a bit of interest in the Boston biotech scene of late. On January 26, the company announced it was buying Bedford, MA-based Avila Therapeutics for $350 million. Last year, Celegene participated in a $30 million funding of Cambridge, MA-based Acceleron and it extended a partnership with Cambridge-based Agios, adding $20 million to a $130 million alliance. In May 2011, Celgene signed on to use Boston-based Foundation Medicine’s genomics testing technology in trials of cancer drugs, with the goal of identifying patients who are most likely to respond well to the medicines.

For Acetylon, the Celgene infusion kickstarts an already ambitious plan for ACY-1215. The company is currently finishing up the first stage of a Phase 1 trial, and plans to begin the combination phase of the trial later this year, Ogier says. The $15 million investment “is significant for a company at our stage,” Ogier says. “It will allow us to augment our cancer program.”

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All the cool kids were doing it, so we just couldn’t resist. We’ve created an Xconomy page on Google+, where we’ll share several of our most interesting stories every day. We’ve also added Google+ sharing buttons to all of our stories here on the site—you’ll find them in the sharing box at right, and at the bottom of each story column.

We’re excited to have another great outlet for our content and a new way to engage with our readers online. We’re looking forward to some lively discussions and debates (and hopefully a few +1′s, too!). So please add us to your circles. Who knows, maybe you’ll even let us crash a hangout or two.

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A young Canadian software startup with Boston investors is now part of a big Boston-area company. Ottawa-based Blaze Software has been acquired by Cambridge, MA-based Akamai (NASDAQ: AKAM) for an undisclosed cash sum.

What’s interesting here is that Akamai, the Web content delivery and networking giant, is making a move into Web performance optimization—basically tackling Web performance at the browser level (what some call “front end”), rather than the network level. Akamai has been positioning itself as a one-stop provider of a secure platform for businesses to reach customers via the Web, mobile, and cloud. That approach also includes, among other things, speeding up Web and mobile applications, as evidenced by the company’s recent acquisition of its California-based rival Cotendo for $268 million.

Today’s deal is no doubt smaller than that, but it could be an important sign of things to come—especially around Boston. Blaze started in 2010, and its seed funding came from local investors CommonAngels and Boston Seed Capital. So why sell now?

“You always have a choice of how you want to grow the business,” says Chris Sheehan, managing director of CommonAngels. “It made a lot of sense for the guys to partner up with Akamai, who’s so strong in the [content delivery network] space. When I made the investment, [Web performance optimization] was just beginning. The timing was sooner than I expected. But in the last 12 months, this whole thing has really started to take off.” [Disclosure: CommonAngels is an investor in Xconomy, and Sheehan is a board member at Xconomy.]

Blaze’s approach is to optimize the code on Web pages so as to speed up the transmission of content and render pages faster on whatever device the customer is browsing on—PC, tablet, or smartphone. This is particularly useful for e-commerce and media sites, which tend to get gummed up by lots of different pieces of code loading on them. The company’s technology (and team) will be integrated into Akamai’s cloud platform, said Rick McConnell, executive vice president of products and development at Akamai, in a statement.

In speeding up websites, Blaze competes directly with Boston-based companies Yottaa (which is also in Boston Seed’s portfolio) and SiteSpect. Google’s team in Kendall Square also released a free tool for Web page optimization in the fall of 2010.

It’s not just about making websites faster, however. All of the above companies have been trying to combine Web optimization with business analytics so as to help businesses track things like sales and customer behavior more effectively. Now Akamai is firmly in the game, and we’ll see how that affects the competitive landscape.

“It’s going to make it a lot harder,” Sheehan says. “It puts a lot of pressure on the other startups.”

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She started her career as a management consultant, but Aubrie Pagano says she always knew she wanted to be an entrepreneur. And she was particularly energized by fashion.

So Pagano spent her free hours assisting local Boston designer Emily Muller in launching her collection, in exchange for the opportunity to get some firsthand experience in the independent fashion design space. There she discovered that designers face a particular challenge—one that would eventually inspire Pagano to create the e-commerce startup Zoora.

“Its hard for independent designers to scale because there’s a discovery issue,” says Pagano. “[Muller] has a great website buts nobody goes to it.”

And as a shopper, Pagano says she’s felt like she’s had to settle for a piece of clothing that just isn’t quite right. Women like her are the perfect customer base for independent designers, she says.

“Something that a lot of people don’t know about independent designers is that they’re really flexible,” Pagano says.

Just last Monday, Pagano opened the Zoora website to the public, to offer women clothing that they can customize to best fit their measurements and taste. Her hope is that the women who feel underserved by traditional retail will bring independent designers the traffic—and business—they so desperately need.

Zoora joins a booming cluster of Boston companies in the space of mass customization, where e-commerce platforms allow shoppers to select and tailor products to better fit their preferences. As my colleague Greg has pointed out previously, these companies offer shoppers personalized jewelry (Gemvara), bags (F. Rock), girls clothing (FashionPlaytes), men’s dress shirts (Boston’s Blank Label and Proper Cloth in New York), and even bras (Zyrra).

Pagano started working on Zoora (a name inspired by “misura,” the Italian word for measurement) last spring, and made hiring a head buyer her first move. Since then, the company has enlisted about a dozen designers (including Muller) to sell garments on the site with options for customization. Another designer is Althea Harper, a former contestant on the Lifetime show Project Runway. (Worth noting, New York fashion tech startup Send the Trend has Project Runway veteran and winner Christian Siriano on staff.)

The customizations to Zoora garments fall into two baskets, says Pagano: “made-to-measure adjustments” and “ready-to-wear tweaks.” With the first category, customers input their specific measurements, which designers take into account to create a garment that’s a perfect fit. With “ready-to-wear tweaks,” meanwhile, garments come in standard sizes, but offer different options for elements like fabric, necklines, sleeves, and hem length.

The Zoora team now consists of … Next Page »

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Yo, is there a ballplayer in the house? Well, there is a House playing ball—professional basketball, that is.

At the age of 33, Adam House, a serial entrepreneur (and shooting guard) who has successfully built and sold three companies—his most recent startup, Velocitude, was acquired by Akamai in 2010—has at least temporarily put aside the tug of entrepreneurship for his love of hoops. More specifically, House has decided to uproot his family from Boston to upstate New York to join the Rochester Razorsharks, a professional basketball team in the Premier Basketball League. Here is his player page).

True, it isn’t the NBA—but House describes the league as very competitive, with most players having come from Division 1 college teams, and several going on to the NBA’s D-League (development league) or playing pro ball overseas. So it’s pretty cool. I caught up with House by phone when he was with the team in Michigan, where they had finished a two-game sweep of the Lake Michigan Admirals. Here is a quick overview of his version of Hoop Dreams…

House grew up in Birmingham, MI, about 25 miles northwest of Detroit. He played basketball for nearby Brother Rice High School, a well-known Catholic school attended by the offspring of many of the Detroit area’s business leaders or auto execs.

But House also had a passion for entrepreneurship. He worked at Rock Financial, a Quicken Loans company, and was able to learn from Dan Gilbert who is now the main owner of the Cleveland Cavaliers. So, bitten by the business bug, he left college (Centre College, a small liberal arts school in Kentucky) after his freshman year at age 19 to work for a direct marketing firm in Florida. He quit that after one year, and in 1998 formed a startup to do direct marketing for financial services companies with $500 of his own money. He built that into a multi-million-dollar business (an Internet lead generation startup he also founded merged with the company) and sold it in May 2007. A few years later, House launched his third startup, Velocitude, a mobile services platform company that enabled delivery of video and other content to mobile devices. He built that up as well, and sold it to Akamai in mid-2010 for undisclosed terms.

But let’s get back to hoops. As part of the Akamai deal, House and his family—wife and now three sons—moved to the Boston area. Among other things, he joined CommonAngels, the angel investor group that is the lead investor in Xconomy. After leaving Akamai, House was not quite ready for the grind of another startup, so he decided to train for a triathlon. “I saw myself in bike pants and a helmet, and I just looked in a mirror and said, … Next Page »

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Plans for IPOs and venture funding dominated the New England deals news this week.

—A new seed fund, backed by venture firm New Enterprise Associates and hosted by Harvard, came out of the woodwork last week. The Experiment Fund will invest up to $250,000 in seed funding in selected startups, with a focus on technologies that come out of Cambridge, MA. The news broke just a few days ahead of Facebook—the one that got away—revealing its plans to go public.

—Radius Health, a Cambridge-based startup working on treatments for osteoporosis, filed paperwork indicating its plans to raise as much as $86 million in an initial public offering.

—A PricewaterhouseCoopers and National Venture Capital Association report shows a mixed picture for life sciences investing in 2011, my colleague Arlene reported. Biotech companies raised $4.7 billion, showing a 22 percent increase over 2010, but the deal volume for the sector dropped 9 percent to 446 transactions. Medical devices companies also showed an increase in funding dollars but a drop in number of deals.

—Cambridge-based Brightcove set the price range of its initial public offering at $10 to $12 per share, according to an amended filing with the SEC. The video hosting startup plans to sell 5 million shares, and give underwriters the option to purchase another 750,000 shares. Brightcove first filed paperwork last August indicating it intended to raise $50 million in an IPO.

—Synchroneuron of Waltham, MA, nabbed $6 million in Series A funding from Morningside Technology Ventures. The startup is developing treatments for movement disorders such as tardive dyskinesia.

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At first glance, a report released last week by PricewaterhouseCoopers and the National Venture Capital Association seems to portend rich times for life sciences startups. Biotech companies raised $4.7 billion in 2011—more than any other sector except for software and enough to help make last year one of the top three years for venture fundraising in the past decade.

But drill down into the report, based on data provided by Thomson Reuters, and the numbers tell more of a mixed story. Total VC dollars poured into the life sciences sector, which also includes medical devices, increased 21 percent to $7.5 billion in 2011. The biotech portion of the haul marked a 22 percent increase over 2010. But the volume of biotech deals dropped 9 percent to 446. What’s more, the medical device portion rose 20 percent in dollar terms (to $2.8 billion) but dropped 2 percent in deal volume (to 339).

What it all means is that VCs in life sciences remain supportive of the sector, but uncertain about its future, says Tracy Lefteroff, global managing partner in PwC’s venture capital practice. “There are still some major challenges ahead in terms of getting the FDA to provide transparency to young companies about what they need to do to get their products out of the pipeline,” Lefteroff says. “For anything [in investing] to be sustainable, FDA issues will need to be worked out.”

Still, some investing trends last year showed clear signs of optimism in life sciences. During the fourth quarter, for example, VC investing in early-stage companies totaled $987 million—a 47 percent jump from … Next Page »

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Cambridge, MA-based Radius Health, which is on a quest to enter the multibillion-dollar market for osteoporosis treatments, said today it has filed to go public. The company hopes to raise $86 million in the proposed offering. The IPO will be underwritten by UBS Investment Bank and Leerink Swann, and co-managed by Cowen and Company and Rodman & Renshaw.

Radius’s lead compound, BA058, is a new type of “anabolic,” or bone-building, drug. In early trials, patients have re-grown bone with little risk of developing hypercalcemia, a dangerous overload of calcium that can result from current treatments. If the drug proves effective in pivotal trials, which the company is running now, it could become a major contender in a very large market. A recent study by Global Industry Analysts of San Jose estimated that the annual market for osteoporosis treatments will reach $8.8 billion by 2015.

The current iteration of Radius’s drug is an injection, but the company is working on a more convenient dosing option—a patch it’s developing in a collaboration with 3M (NYSE: MMM). Using 3M’s “microneedle” technology, Radius developed a patch containing 360 tiny needles that deliver a full dose in about 15 minutes.

Radius last made news in May, when it raised a staggering $91 million and merged with an unlisted shell company in preparation for an IPO. The company’s investors include MPM Capital, BB Biotech Ventures, MPM Bio IV NVS Strategic Fund, the Wellcome Trust, HealthCare Ventures, Scottish Widows Investment Partnership, BB Biotech, Brookside Capital, Saints Capital, Nordic Bioscience, and Ipsen Pharma.

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In enterprise data centers, servers and storage go together like hot dogs and buns. One isn’t much good without the other. But if your specialty is baking buns, you probably don’t spend a lot of time thinking about how to improve the dogs. And that, in essence, is one of the limitations that Hopkinton, MA-based EMC has been trying to overcome lately.

The Hopkinton, MA-based company (NYSE: EMC) is one of the world’s leading vendors of storage arrays for enterprise data centers. Because it has always thought of itself as a storage company, it has never crossed the line into building components for servers. And that’s how, even though EMC was first to market with Flash-based memory technology for enterprises, a much smaller company, Utah-based Fusion-IO, was able to come out of nowhere in 2005 and take the lead in a burgeoning new market for solid-state Flash memory chips for servers. Today HP, IBM, and Dell all put Fusion-IO’s ioDrive cards in their servers; the company went public last year and is valued at around $2.1 billion.

But it’s a natural market for EMC, and it wants in, badly. At an event yesterday in San Francisco, EMC took the wraps off a competitor to ioDrive called VFCache. It’s basically a card full of Flash modules that fits into a “PCI Express” or PCIe slot in a computer server, where it provides an instant memory upgrade. That allows the CPU to get work done faster, without having to slow down to wait for data from the storage array.

EMC's Pat Gelsinger introducing VFCache, aka Project Lightning

How EMC came back from behind in the server-side Flash business is an interesting story of internal innovation. Pat Gelsinger, president and chief operating officer of EMC’s flagship Information Infrastructure Products division, told me yesterday that to help EMC catch up with Fusion-IO, he authorized an unusual skunk works project, with most of the engineering team isolated in EMC’s facility in Tel Aviv, Israel. “We hired the very best people and treated it like an internal startup,” Gelsinger said. “We set incredibly focused goals for the team. We told them not to go to corporate meetings,” but to concentrate solely on “Project Lightning,” the code name for the VFCache product line.

That was the only way to get the job done once EMC had determined that it had to build, not buy, its own alternative PCIe Flash product, Gelsinger says. “Organic innovation is very hard in a big, successful company,” he says. “There are a lot of antibodies saying, ‘No, you can’t do that, we can’t go that fast.’ There are a thousand reasons these things can slow down in a company. So having a very hands-on, top-down focus, combined with a very maniacal, senior, aggressive team, is really what’s required.”

Flash memory, a technology pioneered by Toshiba, is far more expensive than hard drive storage, but it also works much faster. Companies have begun to put extra Flash-based “tiers” of memory between servers and storage arrays in order to address the gap created by ongoing improvements in CPU speeds. Hard drives just can’t read or write data as fast as today’s multicore processors can suck it in and spit it out, which means CPUs are often sitting idle, waiting for data to arrive.

To speed things up, EMC has been adding Flash memory to its storage arrays since 2008—in fact, it has shipped more Flash memory to enterprise customers than all other vendors combined. But before Project Lightning, it hadn’t tried putting Flash into servers themselves, where the benefits are … Next Page »

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Applied Proteomics hasn’t exactly been operating in stealth mode since it was founded five years ago. Co-founders David Agus, a cancer specialist at USC, and Danny Hillis, the MIT-trained computer scientist, gave TedMed talks about the startup’s technology, which provides a 40-gigabyte snapshot of all the proteins circulating in a drop of blood. By pure coincidence, I watched John Stewart’s Feb. 2 interview with Agus last night on “The Daily Show.”

“Danny and David had the foresight to build the tool before trying to use the tool,” says John Blume, a molecular biologist who joined API in 2008 as chief scientific officer. “Although the company wasn’t in stealth mode, the first several years were spent in taking the time to make it right, and then to use it and avoid some of the stumbling blocks.”

Now Applied Proteomics is raising the curtain on several steps that mark its progress beyond a seed-stage startup that was incubating at Applied Minds, an industrial think tank that Hillis founded in Glendale, CA, with a colleague from Disney Imagineering. After moving the headquarters to San Diego late last year, Applied Proteomics is today naming a new CEO—Peter Klemm, a veteran in molecular diagnostics and the former CEO of Lexington, MA-based Predictive Biosciences.

Danny Hillis

The company known as API says it also secured $22.5 million last June in Series B funding from Domain Associates (San Diego partner Jim Blair joined the board), Seattle’s Vulcan Capital, and returning angel investors. Klemm tells me the company raised $4 million from angel investors (who prefer to go unnamed) in what amounted to API’s Series A round in 2007.

David Agus

API’s goal, Klemm says, is nothing less than to “elevate molecular diagnostics to another level beyond the genome” by measuring the proteins made by genes—a long-sought technology that is expected to help doctors improve medical care for individual patients. Because proteins carry out most cellular functions, the company says a snapshot of all the proteins circulating in the body at a given moment represents “the most powerful source of information” in terms of understanding a patient’s health status.

Quantifying all the proteins in the body, Klemm says, can help doctors optimize the course of treatment for individual patients by making it easier to identify the specific drugs that would have the greatest effect on blocking specific proteins or signaling pathways, which can vary dramatically from person to person.

In a statement from the company, Hillis says, “For the first time, we can look at all the proteins in the body with remarkable specificity and sensitivity and use proteomic technology to create … Next Page »

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How are companies spying on each other these days? One of the surprising ways I’ve heard about recently is through the webcam in boardrooms.

That’s right, apparently it’s easy to hack into some companies’ video conference systems, because they lie outside typical security measures. Companies sometimes set up video conferences so they can be accessed directly on the Internet—leaving the door open for eavesdroppers to listen in on meetings, or even remotely monitor a conference room via the camera.

One local software company is helping organizations guard against this threat—and many others. Boston-based Rapid7 is one of the leaders in the growing cluster of IT security companies around town. Rapid7’s approach is complementary to firms like NitroSecurity (recently acquired by Intel/McAfee) and Q1 Labs (bought by IBM), which help organizations guard against security threats in their computer networks and systems.

What Rapid7 does is help organizations find security flaws throughout their IT infrastructure, and then test whether they’ve been corrected. To fuel its growth, the company raised a $50 million Series C round from Technology Crossover Ventures in November—one of the largest tech venture rounds in the Boston area lately. (Rapid7 has raised $59 million to date.)

“There’s a lot of cyber-espionage going on in business,” says Mike Tuchen, Rapid7’s CEO (see photo, left). The activity ranges from stealing sales plans, financial information, and intellectual property, to the aforementioned boardroom eavesdropping, he says. And, of course, it’s not just companies spying on each other; it’s governments and nation states as well, all trying to get their hands on everything from Citibank credit card numbers to the special sauce in Apple’s iPad design.

What’s a CEO to do? If you’re Mike Tuchen, you take a promising company and try to make it better. Tuchen joined Rapid7 as chief executive in 2008. (The company has been around since 2000.) Previously he worked at Microsoft as a group program manager and general manager of SQL server marketing. An engineer by training, he also worked at Sun Microsystems and co-founded Paramark, a dot-com-era online advertising startup.

When he arrived at Rapid7, brought in by Bain Capital Ventures (the firm’s original VC investor), Tuchen saw a company that had “a great engineering and sales team” but not much else. He says he didn’t have to tear up the company, just bring in some key additions: marketing, channel partners, new processes, and a broader product roadmap, including a more international market focus.

So far the effort seems to be paying off. The company has grown to about 240 employees (about half in Boston), and Tuchen says revenues … Next Page »

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If you’ve turned on your TV anytime in the last, oh, decade or so, you’ve no doubt been bombarded by ads imploring you to “ask your doctor” about Drug X. And you’re well familiar with the routine: You get treated to happy images of folks dancing, perhaps, or walking their dogs in pretty green meadows, while a soothing voice in the background tells you that Drug X may cause you to lose your ability to drive safely, lose your vision, or lose your mind.

Forgive the exaggeration but you get the picture.

Well, the FDA isn’t pleased with the pharmaceutical industry’s advertising practices. So it’s proposing a new set of rules that would not only limit the ability of drug advertisers to use so many cheerful images, but may indeed force them to place more emphasis on their products’ potential side effects.

The FDA actually proposed the new rules back in 2010. But it re-opened the matter to public comment on January 27, after it published the results from an experiment it sponsored to measure the impact of distraction on consumers’ ability to understand the risks and benefits of drugs being advertised. The rules would pertain to direct-to-consumer (DTC) ads for prescription drugs on television or radio.

The original proposal is rather bulky. But here are the basics of what the FDA is suggesting: The agency wants to amend the rules for DTC advertising to more clearly define the standards for determining whether side effects are presented in a “clear, conspicuous, and neutral manner.” For example, the new guidelines would dictate that the adds cannot include “distracting representations,” such as statements, images, or sounds that might draw the audience’s attention away from those laundry lists of potentially adverse events.

So what exactly makes an ad distracting? The FDA’s proposal doesn’t really spell it out clearly, but you can get a hint of what the agency was thinking in the newly released report on its study, which it titled, “Experimental Evaluation of the Impact of Distraction on Consumer Understanding of Risk and Benefit Information in Direct-to-Consumer Prescription Drug Television Advertisements.” The FDA planned the study to answer a number of questions. Among them: Do visual images that are positive in tone affect viewers’ ability to comprehend the risks inherent in a product? Do positive images influence how people feel about the product? And if the advertiser super-imposes text onto the images—spelling out the side effects—does that change how viewers perceive the product?

All good questions, to be sure. To answer them, the FDA asked 2,000 consumers to go online and watch an ad for a fake blood-pressure drug called Zintria. But the participants didn’t all see the same ad. Some heard the side effects cited while watching “mildly” positive images (rocks, chairs, metal arches), while others saw “strongly” positive images (babies, puppies, girls jumping with beach balls). Some viewers saw the side effects spelled out in superimposed text, while others didn’t.

Not surprisingly, those who watched cute babies and puppies while hearing about the side effects felt better overall about the product than those who watched the more boring images. Both groups, however, understood Zintria’s risks just fine—and they really got it when the side effects were displayed on the screen in clear text, too.

The FDA has published the study on the Web and re-opened the proposed rules to comments, which the public can submit up until February 27 (instructions below).

We here at Xconomy are plenty distracted by the plethora of peppiness in drug advertising. Here are our votes for … Next Page »

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…or really just one great one: Xconomy needs your help. We’re busy cranking out terrific tech and life sciences journalism and putting on stellar events across the six cities in our network, and we’re looking for a kick-ass marketing coordinator to help us get the word out about all of it.

Full details are here, but in a nutshell: This is a full-time position in our Cambridge, MA, headquarters, ideal for somebody who is happiest when juggling a bunch of diverse projects. We need a person who enjoys figuring stuff out as s/he goes along, and has just enough of the old OCD to pull it off without too many embarrassing typos. Some main areas of focus will include marketing our events, managing our social media efforts, and marketing reprints and premium products.

If doing all that in an extremely collegial, slightly wacky startup environment sounds like your idea of a good time we want to hear from you at jobs@xconomy.com.

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You wouldn’t throw a fancy dinner party in a 7-Eleven. You wouldn’t hold a symphony concert in a subway station, or teach a meditation class on a tilt-a-whirl ride.

So why does anyone expect readers to read long articles on the Web?

Call me a traitor to my kind, but I think the World Wide Web is a terrible medium for long-form writing, precisely because of the mismatch between content and venue. The basic problem is that browsers are for browsing. Today’s commercial Web, where no morsel of exposition is more than one saccade away from a link, a logo, or an ad, is an impossible place to do any deep thinking.

No one designed this outcome. It’s just that the medium grew up so fast, evolving in less than 20 years from a hypertext file-sharing system at a European physics laboratory into today’s infinite digital bazaar. There wasn’t much time to think about whether it really made sense to translate our collective creative output into HTML, dump it onto Web servers, and pay for the whole operation with hyperlinked ads that, by their very nature, take readers away from whatever they’re trying to read.

Fortunately, there are folks scouting for ways out of this mess. Over the last few years, programmer-entrepreneurs like Marco Arment, the creator of Instapaper, have come up with a series of clever applications for separating or “parsing” the Web’s text from its context. This new menagerie of minimalism includes browser-based apps that zap the clutter around Web posts and replace it with a peaceful white background. It also includes mobile apps that let you store these pared-down posts for on-the-go consumption whenever you choose. And in this general category, I’d also include a few new curation services intended to spotlight contemporary and classic long-form writing and make it easier to consume.

I’ve picked 10 of my favorite reading apps and services for quick summaries on the following pages. If you’re like me and you spend a lot of time using the desktop or mobile Web, yet you also love getting lost in a long, thoughtful non-fiction article, then you’ll find some of these services to be life-changing.

But I wouldn’t say that we’ve reached an apotheosis—not by a long shot. At best, the Zen approach to repackaging Web articles is only one element of the solution, and it’s not one that will scale up very well. Already, critics are arguing that this kind of republishing is impolite at best, copyright infringement at worst. As soon as the big online publishers realize how many people are bypassing ads by saving parsed text to Instapaper and the other reading apps, they’ll freak out, the same way broadcasters did when TiVo came along. (It’s no accident that people have called the reading apps “DVRs for the Web.”)

What’s needed now are business models that would make publishers happy about providing more content in these ad-free environments. But we’re a long way from finding payment mechanisms that appeal to readers—let alone equitable ways to split up reading-app revenue between publishers, authors, developers, and platform providers, as a tussle last year between Readability and Apple illustrated (more on that below).

For now, damn the torpedoes—here’s my list of the 10 most interesting and useful reading apps and curation services. I’m going to describe the apps first, because once you understand those, the curation services will make a lot more sense. (For a single-page version of this article that you can export to one of the reading apps, click here.)

First app: Clearly.

… Next Page »

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