SciLink Blog

Tony Williams grew up in Wales, UK - and originally considered being a Welsh teacher. However, after speaking with his career master, Tony quickly decided that career path probably wouldn’t lead to a successful career trajectory. Tony went to Liverpool University where he found Honors Level Chemistry fairly boring and spectroscopy especially challenging. He essentially self-taught himself spectroscopy from books and papers and, as fate would have it, Tony’s protons aligned to find his life’s passion in EPR/NMR spectroscopy. He later saw applications for this technology by studying Vitamin E related systems and this sparked a life long interest in NMR spectroscopy. He went on to get his PhD in NMR applying the technique to study lubricant systems at high pressures up to 5kbar.

Tony’s interest in computers and computing started when he was a poor graduate student. He wrote programs while getting his PhD. to analyze NMR relaxation data and installed PC’s in offices around central London. Tony spent some time at The National Research Centre laboratories in Ottawa performing Single Crystal EPR Rochester and finally landed in New York with the Eastman Kodak company. While at Kodak, Tony was the NMR Technology Leader for the company working with a team of almost 10 NMR scientists and almost as many NMR instruments. While at Kodak, he published over 20 papers and received 2 patents. One of his primary challenges was to homogenize instruments, platforms and processes at the company, specifically for walk-up spectroscopy laboratories so they could maximize throughput and ROI for the chemists. Tony was also one of the three people involved with building WIMS, a web-based information management system (http://www1.elsevier.com/homepage/saa/trac/wimsarti.htm) for managing samples, structure and spectra. This system still prevails today.

While at Kodak, Tony formed a close collaborative relationship with Advanced Chemistry Development (ACD/Labs) on a project to develop NMR based software. After a number of extremely fruitful interactions, Tony decided to take his entrepreneurial spirit out of a Fortume 500 company and into the small start-up company and joined ACD (www.acdlabs.com) as their NMR Product Manager. While at ACD/Labs, Tony managed the majority of their product lines with a focus on structure drawing and databasing, systematic nomenclature and analytical spectroscopy and chromatography. During his tenure he held multiple roles and was the Vice President and Chief Science Officer for a number of years. After a decade at ACD/labs and following the adoption of twin boys a couple of years earlier, Tony found that his demanding travel and work schedule didn’t fit the demands of his young family and started to look for other opportunities.

After seeing the efforts of both PubChem and Wikipedia to deliver chemistry-related data to the public his creative nature determined that maybe a combined approach of both efforts could deliver value to chemists worldwide. His initial concept was for a commercial software product that would crawl a network of disks internal to an organization and index chemistry in documents, reports and other files and integrate with data available on the web. However, Tony believes that a free-access website for indexing chemistry would have more value to Chemists. Thus, ChemSpider was born.

Here are excerpts from the interview:

Why did you found ChemZoo and produce ChemSpider?

[My] intention was always to form a community around chemical structures. We’d like to allow users to annotate and tag information around chemical structures to help share their knowledge and reduce the barriers, both cost, time and navigation hurdles, to chemistry related data. Presently we integrate to well over a 100 chemistry data sources with a few tens waiting to be added at present.

Can you give me some statistics on usage right now?
Presently we’re getting around 6000 users per day, and over 20,000 search requests a day (excluding robots). We’ve got over 1100 registered users but no one has to register to use the site. Those registered users however can add comments, deposit structures, spectra and so on.

How is the company funded?
We’re bootstrapping with personal bank accounts. Also, we have some sponsors who have been kind enough to contribute some donations, generally in exchange for us developing a particular aspect of the site such as extending the API.

Do you have a revenue model?
We’re figuring that out right now and have a number of different discussions with companies right now. This project started as a hobby project as I was gainfully employed at the time it started and never saw it as a source of income. Having chosen the path of self-employment as a consultant the potential of ChemSpider generating revenue is of course of interest. My preference is to not charge the users for public access but to obtain grants, maybe advertising revenue and require fees from companies who with to have secure links to the site for mashing results from ChemSpider data queries with their own internal systems. A rich uncle isn’t an option…I’ve looked across my family tree..

How many people work on the site? Are they full time?
[There are] 5 volunteers working on the site - they are involved with the coding, development of the website, algorithms for structure handling, text mining and so on. Then there are the users who help with “crowd sourcing” of data curation and deposition of new data

What do you want the site to be at the end of the day?

I’d like ChemSpider to be the first place people think of for researching information about small molecules. I work with the Wikipedia chemistry team, and I see our efforts to be complementary. We offer more capabilities however in terms of structure-based searching, hosting of analytical data, services for generation of properties, web-services for companies to integrate ChemSpider to their instruments and into their websites. It would be nice to be “ChemSPider Inside” to coin a phrase from Intel. Based on the interest of groups talking to us now you’ll see growth in the number of chemical vendors putting their catalogs online so it can become a public chemical directory for ourcing chemicals. We’re also working on making open access chemistry articles searchable by chemical structure. We’ve already done work with the International Union of Crystallography to make their open access article available via chemical structure searching. Chemspider is already a content system to aid Open Notebook science with thought-leaders like JC Bradley from Drexel university. We’ve just released the ChemSpider forum to allow the chemistry community to exchange information and collaborate. People struggling with synthesis or class of structures can get into collaborations. We are not short of ideas..bottom line though is that ChemSpider is intended to be one of the central communities to enable collaboration around chemistry and chemical structures

How many compounds are in chemspider?
We have 20 million compounds and growing literally daily.

Highlights?
My career highlights are many. I worked with excellent technical people at ACD/Labs and formed a rich network of friends in the community. Working with Dr Gary Martin from Schering Plough to crack a structure elucidation problem that remained unsolved for over a decade was great and the completion of a review article on Computer assisted structure elucidation that took over 18 months to write was just great.

Who should reach out to you in SciLink?
I pay my bills with consultancy so anyone wanting expertise in cheminformatics, systematic nomenclature and applications of software tools to chemistry is welcomed to contact me. In terms of ChemSpider we are always looking to support our users, extend and improve the system and collaborate with people interested in what we’re doing. I’m especially interested in talking to publishers who might want to deposit to ChemSpider and people who might be interested inus hosting their Chemistry information.

There are a few really interesting groups discussions going on in SciLink right now that I wanted to share on the blog:

Open Access Publishing - Is this a trend that we should all adopt and embrace? What are the benefits to such a model? Finally, what do people believe will be the long term effects of current legislation in this area? You can join the discussion at the Open Access Group Discussion

Damian Gessler writes:

Some aspects of the scientific publishing model remind me of the business model turmoil in the music industry. The status quo in scientific publishing is for taxpayes–to a large but not exclusive degree–to pay for science via government funded grants. To publish the results, one invariably turns over copyright to the publisher, which then sells access. The publisher is providing a service–publishing the results–but the unintended (or intended) consequences of restricting access to government-funded research is the Achilles heal of this business model in the internet age.

From the publishers’ perspective, there is no advantage to restricting access per se; indeed, they should be trying to maximize access so as to drive their relevancy. But of course the *do* restrict access to protect the revenue stream. This is a troubled business plan because it relies on inherent contradictions that yield practices contrary to the wishes of the customer.

Public Library of Science (PLoS) is one threat that is weakening the old model. So is the pay-for-open-access option that some journals offer. Still others address the issue by restricting access for a limited period after publication–such as 6 months. After that access is open.

So how to build a new revenue stream? Deliver value through the most convenient channel to your customers. That means dissassociating revenue from the content–the scientific papers per se–and attach it to the access via indirect channels. Deliver free content from a web site that supports advertising, email, forums, job postings, value-added scientific search, etc. Associate revenue to a net business model built upon page views and click throughs, driving viewership by the free access to the quality scientific content delivered from the journal. This would be a hybrid model between PLoS and old-school publishers.

Pharmacovigilance Group

Robbert Manen started the Pharmacovigilance group to provide a:

Platform for scientists, physicians, regulators and others interested in making medicinal products and medical devices safer.

Finally,

Roop Kaw’s Perioperative Medicine Group is growing (10 members)! You can join him here
Join Roop Kaw’s Perioperative Medicine Group

In a previous post, I wrote about our vision for the SciLink system. One of our goals is to provide a high quality job board where hiring managers can post interesting opportunities to find the most highly qualified candidates. To that end, we have taken steps to make our job board more visible to search engines by posting our jobs on an external page. You may find the job board at:
SciLink Job Board

Over the next few weeks we will start augmenting the page found above with some great new tools to let you leverage the full power of your network.

Stay Tuned!

-Brian

In the United States today more patients are having elective surgical treatments than ever before, 32.7 million in year 2006. Surgical innovations have made not only the recovery process quicker but as many as 75% of the elective procedures done today are done as outpatient procedures. Comprehensive perioperative risk assessment and focused postoperative medical management are increasingly becoming an integral and indispensable part of quality surgical care today.

The average surgical patient today can be older and more obese. Preoperative medical complications are common in patients of advanced age and those with co-existing medical conditions like hypertension, diabetes, heart disease and obesity, just to name a few. These complications worsen surgical outcomes and increase the cost of care. As perioperative patient care protocols expand to include a wide variety of medical morbidities, some clinicians with traditional medical or anesthesiology training feel unprepared to serve as medical consultants for or co-manage surgical patients. At the same time awareness of newer risk factors for postoperative complications with increasing age and obesity is important.

Meet Roop K Kaw MD, an Assistant Professor with the Cleveland Clinic Lerner College of Medicine and Department of Hospital Medicine, Medicine Institute, at the Cleveland Clinic. He recieved his medical degree from the University of Kashmir, India in 1990. He is board certified in Internal Medicine and an associate of the American College of Physician Executives.

He is actively involved in research in the area Perioperative Medicine and Outcomes. His current research focuses on novel predictors of cardiopulmonary risk in patients undergoing major surgery. Dr Kaw is currently funded by the NINDS (NIH) for studying the incremental risk of Sleep Apnea in cardiac surgical patients and the role of Crystal-20 monitor in inpatient Sleep studies. Dr. Kaw is widely published and serves on the editorial board of several medical Journals. He has presented his research both nationally and internationally.

Dr. Kaw serves on several national committees and advisory boards. He is a member of the Research committee for the Society of Hospital Medicine and co-chaired the scientific abstract committee in the 3rd Annual Perioperative Summit at the Cleveland Clinic. He also serves on the Advisory Board of Gerson Lehermans Council of Health Care Advisors and Reuter’s Insight an independent international research consultancy

Who should contact Dr. Kaw?

Anyone interested in Perioperative Medicine should join him on SciLink and also join the new Perioperative medicine group. See you all there!

Update

The SciLink Perioperative Medicine Group is growing:

Loading from scilink.com

I had the pleasure of interviewing Carl Zimmer in early May of this year. I took a bit of pleasure turning the tables on this intriguing science writer, as you could imagine, he hadn’t been interviewed too many times in the past. Although my interview was brief, I was able to glance into Carl’s world and passion for science. We explored a number of topics from the mundane (what it takes to get into science writing) to the publishing industry and finally to his incredibly interesting book on E.coli. What I found most fascinating about Carl was his complete lack of salesmanship and ego. You see, Carl is known in science writer circles as a force to be reckoned with. The New York Times Book Review calling him, “as fine a science essayist as we have”. I imagined all kinds of different scenarios unfolding as I picked up the phone to dial Carl’s number: overbearing ego maniac, super being who was too busy and bored to take my call etc. But surprisingly, none of these scenarios played out. Carl Zimmer is soft spoken, often self deprecating and extremely generous with his time. No ego here, just a man with a passion for science and nature. And, yes, he’s wicked smart.

Here are some excerpts from our interview:

How did you get into science writing?
[I] was at Discover magazine, just trying to get in to magazine world.. Once I started there, I found out that I really enjoyed science writing, and I haven’t stopped since.

What is/was your favorite topic in science right now?
I’ve just written a book about E.coli. I guess you could call me E.coli’s missionary. The book tries to show how much cool biology is packed into such a tiny thing. It can sense chemical and temperature gradients and integrate this information as if it had a brain. It can use this information to navigate through its environment. Engineers are getting obsessed with E. coli because the way its genes and proteins interact reminds them of auto pilot systems. When you learn about E.coli [you’re] really learning about the entire history of molecular biology.

How do you feel about open access publishing like PLOS/BMC?

I blogged about this here. I believe that open access papers will get more coverage in old and new media than papers published in traditional subscription journals. There are huge time advantages in reading open access journals. I can Google for a topic and in 2 seconds can be reading the entire article. If I come across a paper in a closed journal, I can’t get it immediately. The extra steps involved will inevitably push people toward open access models.

Another factor playing in open access’s favor is that it doesn’t create pointless conflicts between a journal and the people who write about what’s in it. One striking example involved a blogger who had written about a paper sourced from a subscription journal: This individual reproduced a figure and got an email threatening legal action. This looked really bad for the publisher and [the] blogosphere revolted. If I write a piece that is sourced from a PLOS (http://www.plos.org) paper and reproduce a figure on my blog, I know I won’t be harassed.

Any pointers for other up and coming science writers?
People really need to learn how to write. Spend the time training through internships, graduate school, freelancing etc. You have to spend the time practicing your craft. This is a really interesting time to be a science writer but conventional opportunities are disappearing so try to be as creative as you can. Try to write every day whether you have an assignment or not. My best piece of advice is that no one can read your mind: Very few people have PhD’s in your area so start with that premise and the clarity of the story.

Who should reach out to you in SciLink?
I’m interested in connecting with Biologists and Earth Scientists who need help telling their story.

Check out Carl’s Publications:
My Book - Microcosm
My blog - http://www.scienceblogs.com/loom/
My website – http://www.carlzimmer.com

Brad Langhorst, 33, grew up in Denver, Colorado where his father worked for General Motors as an Engineer. During his junior year in high school, Brad’s father was transferred to Michigan where there was a gym requirement. Having played sports in high school, he had no gym credits and he didn’t want to spend his entire senior year in gym shorts. Cleverly, Dr. Langhorst looked for alternatives and found the School Year Abroad program in Barcelona, Spain that would allow him to finish high school and experience more of the world. After winning an appointment to the U.S. Naval Academy, Brad thought the curve-balls were behind him. But, in a strange twist of events, he lost his appointment due to a medical disqualification. Scrambling for another option, Brad applied and was accepted to Johns Hopkins University. After spending some time there Brad decided the famous JHU “pressure cooker” wasn’t for him and transferred to The University of Connecticut where he worked at the National Analytical Ultracentrifugation Facility. After UConn, Brad heard about the human genome project and thought “if I don’t participate in this it would be like living in the 60’s but not going to Woodstock”. He joined the genome project at the Whitehead Institute Center for Genome Research and deferred his grad school aspirations. After his stint at Whitehead working on gene-disease association studies he started a Ph.D. program at the University of New Hampshire to work in Tom Laue’s lab. To balance his long-term scientific goals with some more immediate impact on the world, Brad and some friends started CoopMetrics while in graduate school. By applying scientific data reduction and analysis techniques to financial data, CoopMetrics has been able to provide cooperatives of local businesses with analytical tools to help them compete with chains. Having just finished his doctorate and with CoopMetrics large enough to sustain its growth without his day-to-day input, Brad has begun his search for the next curve.

We had a chance to ask Dr. Langhorst a bit out his work and future as a newly minted Ph.D. in an economic downturn:

What interests you in Science?

While the first large scale step in understanding how life works is the genome project, as Eric Lander says: It’s just a parts list. Interactions between proteins and other molecules, as the major effectors of biology must be understood in detail if we are to move from tinkering to engineering. Projects like UniProt, HUGE and PRIDE are building the catalog of proteins and their interactions but don’t address the details of the interactions. The Research Collaboratory for Structural Bioinformatics collects structural information about proteins in the Protein Data Bank. Understanding the energetics of a molecular interaction under specific conditions is an inherently low-throughput endeavour but it is required if we are to tell the difference between interactions that effect change and those that are a result of happenstance. Only detailed studies of the individual interactions can provide sufficient detail to draw these important distinctions. If we can connect the large scale efforts mentioned above with the individual experiments on protein interactions performed in labs all over the world, we’ll be able to construct a valuable resource to allow someone to understand the entire network of interactions that takes place when Molecule X interacts with a protein. PANDaS (Protein Association Network Data Server) is the result of my dissertation work collecting Analytical Ultracentrifuge data and analyses, it is a first step toward my long term vision of understanding the entire network of important protein interactions in enough detail to make predictions.

What did you learn were your strengths in grad school?

Early in grad school, my family called me “5 projects”; I like to work in parallel to hedge against bad ideas, but at some point you have to focus on one to make real progress. In graduate school, I learned how to strike a balance between keeping options open and diving into the most promising option.

What are you looking for in your next career move?

I’d like to work with people doing large scale data discovery and integration. My dissertation work involved aggregating protein association studies and storing/analyzing them in a database. I’d like to use the analytical and informatics skills I honed in grad school in a new area during this next step. This was one of my main reasons for joining SciLink - to identify potential collaborators and/or employers who share my interest in understanding biology with enough depth to make intelligent interventions. I loved working at Whitehead where there was a collection of smart people with varied experience and interest working toward roughly the same goal. I’d like to find a similar experience.

So is that your dream scenario then?

My dream job would allow me to extend my dissertation work from Analytical Ultracentrifugation to other solution techniques like Surface Plasmon Resonance, Light Scattering, Calorimetry or Electrophoresis. I’ve built a framework tools to collect data and analyses but this is too big a project to complete on my own. I hope I can find a group of like-minded people who can fill in the gaps in my expertise benefit from my experience.

I guess you could call what you’d like to build the “Protopedia”?

I hadn’t thought of it that way but the idea is a lot like Wikipedia in that it concentrates the efforts of many scientists to build something valuable.

Who should reach out to you in SciLink?

I just finished my Ph.D. so I’m looking for opportunities where I can utilize my analytical and computation skills. Collaborators, recruiters in both academia and the pharmaceutical industry are welcome but I’m interested in connecting with anyone who shares my interest in understanding protein interactions.

Chavonne Jones, 24, always had a penchant for science and education. She recalls an early memory while in high school, “we were assigned a group project about something environmentally related. A NOVA program came on TV about genetically engineered foods. It was then that I became completely fascinated with genetics and genetic engineering.” She would go on to take part in many school activities seeking out ways to combine her love for science and education. It was those early days that helped shape Chavonne’s work and life’s passion: The education and dissemination of genetic information as a genetic counselor.

Chavonne enrolled in the genetics program at Nevada School of Medicine in Las Vegas where she has been for the past 2 years and runs the website, www.humangeneticsdisorders.com that, “is committed to genetics education awareness. To obtain a better understanding about genetic revolution, we provide the history of genetics. The latest information on all human genetic disorders from Achondroplasia to Wilson’s disease is available. Other areas of focus include: dna and rna sequencing, stem cell research and therapy, genetic testing and screening, genetic selection, genes and behavior, mental health, gene therapy, cytocogenetics, pharmacogenetics, xenotransplantation, cloning, ethical, legal, and social issues in medical genetics.”

Ms. Jones enjoys taking part in the Genetic Alliance – an organization dedicated to genetics education and participates in the American College of Medical Genetics and is interested in a variety of genetics oriented topics including: gene therapy, biotechnology, plant genetics cytogenetics and stem cell therapy.

Chavonne is specifically interested in reaching out to those who are working in these fields to help her translate current research and discoveries to those in need. To contact her, join her SciLink network by getting in touch with here.

This is just a brief note letting you know about some fun and exciting SciLink updates. Here’s the executive summary:

• New Job Board - We’ve updated our job board making it much more user friendly. You can post job openings for free until July 1st.
• SciLink Videos - We scoured the web and found some really fun and interesting talks. Want to suggest a video? Contact us at: connect@scilink.com. Videos are on your dashboard enjoy!
• Group Page Update - We updated the group pages to make it easier to search for groups you may be interested in. We’ve also started to categorize groups. Group owners can categorize their own groups if we haven’t already.
• Featured Groups - We’ll be featuring groups that we find interesting and posting them on the main group page. Those groups with more participation will be posted there
• Sponsored Groups - want to sponsor a group? Contact us at connect@scilink.com for more information
• Dashboard Update - Groups your network has joined is now a new widget on your dashboard. You can now see what groups your network has become part of
• We re-added the Citation Manager to the navigation section - The citation manager allows you to find and store bookmarks to interesting content on the web. It automatically recognizes a number of different journal websites and will download abstracts for you.

Enjoy!

Many of you have been asking me on and offline why I started SciLink and where I would like to take it. I will try and answer the first part of the question and give you my best case scenario for SciLink as the answer to the second half.

Why did I start SciLink?

I’ve been writing scientific software for over 10 years using different technologies, architectures, visual interfaces etc., with the intention of providing scientists and clinicians a way to enhance their understanding of each other, their work and its impact on society. I believe the dissemination of scientific information and discovery is every scientists’ social obligation. This is especially true of those scientists whose salaries, laboratory equipment and employees are funded by government tax dollars. But what really drives me is a much more personal and selfish endeavor: I would like to hasten the discovery process by organizing scientists around the globe. I have a particular interest in finding and securing jobs for the research community - SciLink’s mission is to help you find a place to do your best scientific work. The reason? It’s very simple. My family and I have been affected by crohn’s, diabetes and heart disease. I believe that science is the engine by which all health, technological and social innovation occur. Therefore, I have made it my life’s work to provide you with the best website in the world to find colleagues, potential collaborators and amazing work opportunities. I have no doubt that one day you will make a connection in SciLink with a new colleague, collaborator or friend who helps you think through a new strategy in the lab, provides a new computational method or statistics advice. I am confident that these connections will help transform and enhance our scientific knowledge. Who knows, maybe that connection will help my family and I too.

Where are we taking SciLink?

That’s partly up to me and partly up to you. I have some very big plans for the SciLink website. I hope SciLink comes to be known as the number one destination for scientists to find new relationships, jobs, colleagues and more. But I want this company to be more than that. I want to help philanthropists find interesting projects to fund, help clinicians find new partners in their fight against disease and debilitating disorders, help publishers find a well of interesting researchers and potential editors and venture capitalists a way to identify interesting new technologies on the horizon. All these wishes can come true through your participation in the SciLink adventure. You can help us by letting others know SciLink exists, sending invitations and providing valuable feedback.

Here’s the best news of all: You’re already doing it! We’ve seen a tremendous amount of participation. Last month alone you helped us sign up over 2,000 new SciLink users! Thanks so much for doing that. As I stated in my previous email, our goal is to get to 100,000 users by the end of the year. Please help out by sending out invitations to your friends and co-workers!

Thanks for using SciLink, thanks for making a better world.

Yours,

Brian Gilman

Founder & CEO

SciLink Inc.
View My SciLink Profile

As I mentioned in a previous blog post, we added the ability for you to draw chemical structures in the “edit profile” section of the site and associate those structures with your blog. I am pleased to say that a fair number of users have been drawing structures and putting them into their profiles. One user, William Gunn took some time and drew a very large structure. Can you figure out what it is and why it’s funny? Take a look below: