SciLink Blog

May SciLink Updates and Announcements
File Sharing Comes To SciLink!
We are pleased to announce the addition of file sharing to the SciLink platform. You can now upload files to your profile and send these files to groups that you have joined. If the file is an image, it will become instantly viewable in the new SciLink image viewer. Right now, files are either publicly accessible or only viewable by members of your network. In the future, we’ll be adding a more fine grained permissioning scheme.
We have also added file uploading and sharing to the groups section of SciLink. We believe this will help groups share any pre-publication material, images, word documents, spreadsheets etc. Anything you need to get your work done can be shared in the file upload section on SciLink!
Finally, we have fixed a number of outstanding bugs on the system and made it easier to complete your profile by adding an autocomplete capability in the expertise, school and work sections.
Thanks so much for using SciLink!

We’re switching our servers to Amazon’s cloud. This has been a bit of a slow process and has caused some downtime of our service. We believe that this switch will aid in our future up time, responsiveness and scalability. More importantly, we will be able to better respond and maintain our private channel partner websites by spinning up “clones” of the SciLink service with a flick of a switch. We’re very sorry for the delay and will be up this weekend.

Thanks for your continued patience.

Sincerely,

Brian Gilman
Founder & CEO
SciLink Inc.

Can it be true? Are all of us blue? We’d like to know here at SciLink. Help us out by logging into your account and cast your vote! You need to have an account to vote. We’ll publish our results after we perform our analysis on November 5!

Here’s an interesting tidbit from ScienceBlogs:

In the latest issue of Science, an article on grass-roots efforts by scientists in the last weeks before the election brought up a startling point, that there have been a lot of letters to the Editor and OpEds published in newspapers either endorsing Obama or pointing out the errors of the McCain campaign rhetoric on science. What is absolutely amazing, is that there has not been a single letter or OpEd by a scientist endorsing McCain. Not ONE? Here is a partial list of OpEds and letters that have appeared. This is by no means a comprehensive list. In fact, these are almost all in battleground states. This is a really unusual thing to happen in an election and should be appreciated for sheer volume.

Truly Amazing - Enough Said…

If you haven’t heard, we recently updated the site with events, meetings and conference listings. At SciLink we’re trying hard to keep you up to date with the scientific world and your network. We do this in a number of different and complementary ways. First, your dashboard is a portal into all the activity in SciLink. We feed global activity to you: new jobs, events and groups that have been created so you know what’s going on in the SciLink community and don’t need to go to a hundred web pages to try and figure it out for yourself. Next, we roll up your network’s activity by funneling the papers your network is reading, events they are attending and groups they’ve joined. All these features let you keep abreast of what’s going on in your community.

The event, conference and meetings part of our site gets you even more connected by allowing you to plan and share what meetings and events you are interested in. It even helps find events that you might never have known about before!

Right now SciLink lets you rate and create comments for events you’re attending. We plan on more interesting features in the near future. So, why not take a look right now? It’s simple to get started! Click here to see a listing of conference, events and meetings!

If you’re planning a meeting or event head on over and post and event today!. SciLink is a great way to get the word out!

This is an unprecedented amount of money to provide to a research institution. I think people forget just how amazing Eric Lander is as an executive and business person. You couldn’t ask for a better science based executive. Read below:

Less than five years into a ten-year groundbreaking experiment in philanthropy and science, the results are in. The Broad Institute of Harvard and MIT, which was founded in 2003 and launched in 2004 to test how effective venture philanthropy and inter-institutional collaboration could be in propelling biomedical progress, has been declared a resounding success, and will now become a permanent, standalone institution within the biomedical landscape.
At today’s celebration of its anniversary, the Broad Institute of Harvard and MIT received an unprecedented gift from its philanthropic founding partners Eli and Edythe L. Broad: an endowment intended to establish the Broad Institute of MIT and Harvard as a permanent biomedical research organization. Eli and Edythe Broad announced their gift this morning at a ceremony featuring speeches by Governor Deval Patrick of Massachusetts, MIT President Susan Hockfield, Harvard President Drew Gilpin Faust, Nobel Laureate David Baltimore of Caltech, and Broad Institute director Eric Lander.
The unequalled $400 million endowment gift brings the Broads’ total commitment to $600 million. The gift is a testament to the success of the institute’s new model of research collaboration that spans the entire MIT and Harvard communities, including the 17 Harvard-affiliated teaching hospitals. This model of collaboration aims to accelerate the pace of scientific progress and make data and tools rapidly and freely available. In its short history, the Broad Institute’s accomplishments include cataloging and identifying genetic risk factors for diseases such as type 2 diabetes and autism; discovering new therapeutic targets for cancer, malaria, and other diseases; and applying genomic tools to better understand and treat human pathogens like tuberculosis.
“Of all of our philanthropy, the Broad Institute has been the investment that has yielded the greatest returns,” said Eli Broad, founder of The Eli and Edythe Broad Foundation. “This truly is a new way of doing science, and the Institute’s unique collaborative model for scientific research has resulted in remarkable accomplishments in a very short period of time. Although this is a large gift – the largest that we have ever made – it is only a fraction of what will be needed to unlock the enormous promise of biomedical research at MIT and Harvard. We are counting on others to step forward as partners in the next phase of this grand experiment. We are convinced that the genomics and biomedical work being conducted here by the world’s best and brightest scientists will ultimately lead to the cure and even the prevention of diseases.”
The Broads’ $600 million commitment is the largest to support biomedical research at a university anywhere in the world. The Broads initially invested $100 million in 2003 as a way to test the institute’s new approach to biomedical research. By 2005, the Broad Institute had already made significant accomplishments and progress, and the Broads’ invested a second $100 million. Their endowment of $400 million today will allow the Broad Institute to transition to a permanent, non-profit 510(c)(3) organization with both Harvard and MIT still at the heart of it, continuing to help govern the institute.
“Eli and Edythe Broad are true visionaries,” said Eric Lander, founding director of the Broad Institute. “They made an enormous bet in 2004. Their bet has paid off more handsomely than any of us imagined. It has unleashed the creative potential of a remarkable community of scientists. And, it has defined a new model for how scientists and institutions can work together.”
“There is no place in the world with as great a concentration of life sciences talent, resources, and vision as Massachusetts,” said Deval Patrick (D), Governor of the Commonwealth of Massachusetts. “With this significant endowment of the Broad Institute by Eli and Edythe Broad – and the collaboration and support of the industry, academia, business, and government through the Massachusetts Life Sciences Initiative – we are on our way to helping find new cures for diseases, creating new jobs, and positioning ourselves for long-term economic growth.”
“To fully realize the benefits of the genomic sciences, scientific research must transcend the boundaries of disciplines, departments, and even institutions,” said Harvard University President Drew Gilpin Faust. “Through their continued philanthropy, the Broads have made that transcendence possible. I am grateful for their support of this important work and look forward to continuing our partnership with the Broad Institute.”
“Cambridge and Boston are world-renowned for their creative, scientific minds and unrivaled biomedical community, and the Broad Institute is uniquely positioned to realize the full potential of these intellectual resources,” said Susan Hockfield, president of MIT. “We are profoundly grateful to Eli and Edythe Broad for their generosity and vision, and look forward to continuing our many collaborative research efforts through the Broad Institute and defining the future of the field.”

We’re still at it, making general improvements to the site, fixing bugs and adding features. As usual, here’s the executive summary:

• We partnered with Simply Hired  to give you the best and most comprehensive scientific job board on the web. 
• Check out “Job Trends” which was also made available through our partnership with Simply Hired. 
• We are also working with jobster to provide you with interesting science and clinical jobs
• The dashboard has been revamped to better categorize scilink activities and updates
• You will a constant and consistent navigation section in the top left hand side of every section of the website
• We’re gathering even more interesting news from around the blogosphere and web to keep you up to date with the latest and greatest scientific topics and discoveries 
• Our citation manager has been updated allow you to share citations with your network! You simply click on the names of friends and colleagues you would like to share with, everything else is taken care of for you. 
• The citation manager now reports the number and name (with a link to their profile) of people who have also citied a link, article etc. 
• Widgets, Widgets, Widgets! Click on the profile section of the website and choose “share” on the left hand nav to allow you to put a brief biosketch on your own website. 

Here’s an example of our SciLink widget: 

Loading from scilink.com

Those are the major changes. There are lots more coming that we are excited to share with you. Until my next blog post!  -Brian 

None of us in the first world have the time. We don’t have the time to do all thing things we’re supposed to do. We’re too busy consuming. Yet one person has made it his life’s work to find the time to make sure the poor get proper healthcare. I have come to know that man through a book called, “Mountains Beyond Mountains”. Which, in Haitian means, “you’re screwed”… I encourage everyone reading this blog post to pick this amazing book up and, if you can find the time, watch this video.

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.