Conmergence

2008 Fiber To The Home Conference & Expo September 21 - 25, 2008 Gaylord Opryland® Resort & Convention Center, Nashville, TN

<ed.note>The conference's theme is "Linking Communities at the Speed of Light" but more intriguing to me is the the scheduled appearance of Don Tapscott (The Naked Corporation: How the Age of Transparency Will Revolutionize Business, Digital Capital: Harnessing the Power of Business Webs, Creating Value in the Networked Economy, Blueprint to the Digital Economy: Creating Wealth in the Era of E-Business, Growing Up Digital: The Rise of the Net Generation, The Digital Economy: Promise and Peril in the Age of Networked Intelligence, Who Knows: Safeguarding Your Privacy in a Networked World, Paradigm Shift: The New Promise of Information Technology)  adreessing his latest work, Wikinomics How Mass Collaboration Changes Everything. Implicit in Tapscott's writings is management's buy-in of the distrubuted digital enterprise-enabled results-only collaborative work environment. If you happen to be one of those creatures (especially if you are from Nashville), I invite you to join the Linkedin.com Project Net-Work group and Technology Nashville.</ed.note>

Sunday, September 21, 2008
1:00 p.m. - 5:00 p.m.	Registration Opens
Monday, September 22, 2008
7:00 a.m. - 5:00 p.m.	Registration Opens
8:00 a.m. - 1:00 p.m.	Developer Panel Workshop  *Additional fee*
8:00 a.m. - 1:00 p.m.	Home Networking Workshop  *Additional fee*
1:00 p.m. - 1:45 p.m.	Track Session - Series 100  *Conference Pass and Day Pass attendees only*
1:00 p.m. - 1:45 p.m.	FTTH Executive Summit *By invitation only* Moderated by: Don Tapscott, Author
2:00 p.m. - 2:45 p.m.	Track Session Series 200  *Conference Pass and Day Pass attendees only*
3:00 p.m. - 7:00 p.m.	EXPO Grand Opening & Opening Reception *Open to all registered attendees*
Tuesday, September 23, 2008
7:00 a.m. - 5:00 p.m.	Registration Opens
7:00 a.m. - 8:00 a.m.	Continental Breakfast *Conference Pass and Day Pass attendees only*
8:00 a.m. - 10:00 a.m.	Opening General Session    *Conference Pass and Day Pass attendees only* Keynote Speaker - Don Tapscott, Author Wikinomics: How Mass Collaboration Changes Everything Sponsored by: FTTH Council Awards Sponsored by: FTTxcellence Awards Sponsored by:
10:00 a.m. - 10:15 a.m.	Refreshment Break    *Conference Pass and Day Pass attendees only*
10:15 a.m. - 11:30 a.m.	Global Carrier Keynote Panel   *Conference Pass and Day Pass attendees only*
11:30 a.m. - 3:30 p.m.	EXPO Hall Opens   *Open to all registered attendees*
12:00 noon - 2:00 p.m.	Luncheon in EXPO Hall  *Open to all registered attendees*
3:15 p.m. - 4:45 p.m.	ITCo Panel  *Conference Pass attendees only*
3:15 p.m. - 4:00 p.m.	Track Session Series 300  *Conference Pass and Day Pass attendees only*
4:15 p.m. - 4:45 p.m.	Track Session Series 400   *Conference Pass and Day Pass attendees only*
5:00 p.m. - 5:45 p.m.	Track Session Series 500   *Conference Pass and Day Pass attendees only*
6:00 p.m. - 8:00 p.m.	International attendee Reception   *By invitation only*
Wednesday, September 24, 2008
7:00 a.m. - 4:00 p.m.	Registration Open
7:00 a.m. - 8:00 a.m.	Continental Breakfast  *Conference Pass and Day Pass attendees only*
8:00 a.m. - 9:00 a.m.	Government and Regulatory Panel
8:00 a.m. - 8:45 a.m.	Track Session Series 600  *Conference Pass and Day Pass attendees only*
9:00 a.m. - 9:45 a.m.	Track Session Series 700  *Conference Pass and Day Pass attendees only*
9:45 a.m. - 10:00 a.m.	Refreshment Break  *Conference Pass and Day Pass attendees only*
10:00 a.m. - 10:45 a.m.	Track Session Series 800  *Conference Pass and Day Pass attendees only*
11:00 a.m. - 12:15 a.m.	Panel Session Series 900  *Conference Pass and Day Pass attendees only*
12:15 p.m. - 1:00 p.m.	On Own for Lunch
1:00 p.m. - 4:00 p.m.	EXPO Hall Opens
4:15 p.m. - 5:45 p.m.	Closing General Session with Keynote Speaker  *Conference Pass and Day Pass attendees only*
7:00 p.m. - 10:00 p.m.	EXTRAVAGANZA - Closing Reception with Entertainment *Additional fee* "Don't forget your dancing boots!"
Thursday, September 25, 2008
8:00 a.m. - 4:00 p.m.	Post Conference Workshops

European Commission Marie Curie Initial Training Networks Call For Proposals

The European Commission has published a call for proposals under the 'People' section of the Seventh Framework Programme (FP7). The call relates to the Marie Curie Initial Training Networks (ITNs), which are intended to improve the career perspectives of early-stage researchers in both the public and private sectors, thereby making research careers more attractive to young people.

This will be achieved through a trans-national networking mechanism, aimed at structuring the existing high-quality initial research training capacity throughout Member States and Associated countries in both the public and private sectors. It will be implemented by supporting competitively selected networks of organisations from different countries engaged in research training.

The networks will be built on a joint research training programme, responding to identified training needs in defined scientific or technological areas, with appropriate references to interdisciplinary and newly emerging supra-disciplinary fields.

The action is primarily for researchers from Member States and Associated countries, but is also open to researchers from third countries.

The budget for the call is €185,000,000.

The deadline for submitting proposal documents is 2 September 2008 at 17:00:00 (Brussels local time).

Further information here.

U.S. Department of Labor Dictionary of Occupational Titles Call for Participation

We are writing to request your assistance with an important program sponsored by the U.S. Department of Labor (USDOL) known as the Occupational Information Network (O*NET). The USDOL is gathering occupational information in an effort to better define worker and work characteristics such as knowledge, skills, abilities, activities, and work context for nearly 900 occupational categories in the U.S. economy. As the data is collected and published, it will be used by millions of employers, workers, educators, and students (http://online.onetcenter.org). Much of the information already is in use by agencies and organizations across the nation (http://www.doleta.gov/programs/onet/oina.cfm).

The O*NET program is seeking experts in the occupations of Bioinformatics Scientist, Bioinformatics Technician, and Biostatistician.  The last complete update of the Dictionary of Occupational Titles was conducted by USDOL in the late 1970s. Basic criteria includes that data be provided by individuals who have performed the occupation for at least one year, have a five or more years of experience in the notedoccupation, andhave performed in that same arena duringthe past six months. This can bepracticing, consulting, teaching, instructing, supervising, etc. A short description of the occupation currently being updated is listed below. Please use the description, not the title, to decide if you may be a good match:

Bioinformatics Scientists:  Conduct research using bioinformatics theory and methods in areas such as pharmaceuticals, medical technology, biotechnology, computational biology, proteomics, computer information science, biology and medical informatics. May design databases and develop algorithms for processing and analyzing genomic information, or other biological information.

Bioinformatics Technicians:  Apply principles and methods of bioinformatics to assist scientists in areas such as pharmaceuticals, medical technology, biotechnology, computational biology, proteomics, computer information science, biology and medical informatics. Apply bioinformatics tools to visualize, analyze, manipulate or interpret molecular data. May build and maintain databases for processing and analyzing genomic or other biological information.

Biostatisticians:  Develop and apply biostatistical theory and methods to the study of life sciences.

The Bioinformatics Organization, Inc. is asking for volunteers from our membership to assist in the collection of information about these occupations.  Please be assured that your decision regarding participation in O*NET will not impact your standing as a member of the Bioinformatics Organization, Inc..

RTI International (RTI), a nonprofit research firm, is assisting USDOL with the O*NET data collection effort.  Please send an e-mail indicating your interest to participate, including your experience, title, last name, first name, address 1, address 2, City, State, ZIP code, day time Phone number, and Bioinformatics Scientist, Bioinformatics Technician, and Biostatistician area of specialty to Ron Wandscher, Business Liaison, at rwandscher@onet.rti.org.  You can also call 877-233-7348 ext. 108.

By participating, you will contribute to a key resource providing our nation with continuously updated occupational information.  Thank you in advance for your time and effort.

Council for Entrepreneurial Development’s Tech 2007 Conference - October 10-11, Chapel Hill, NC

The Conference will explore the future of emerging and converging technologies that are reshaping today’s hottest industries. Now in its 17th year, the Tech Conference will focus on the latest cutting-edge markets and global opportunities in clean technologies, gaming and digital media, medical devices, new materials, nanotechnology, telecom, internet, software and hardware and more. Attendees will be inspired by speakers and panelists including Najmi Jarwala, president of Sony Ericsson Mobile Communications USA; Edward Iacobucci, CEO of DayJet Corporation; and Don Dodge, director of Microsoft’s Emerging Technologies division and author of the blog, The Next Big Thing. Tech’s Demo Pavilion will serve as a launch-pad for over 35 innovative technologies from entrepreneurial companies, university groups, corporations and research institutions from across the Southeast and Mid-Atlantic. And, new this year, the hottest gaming technology companies will showcase their innovations at a special reception. Visit http://www.cednc.org/tech to learn more or call (919) 549-7500.

2nd Nano App Summit, Ritz Carlton, Cleveland, October 22 - 25, 2007

Nano App 2007 is the most applications focused nanotechnology event of the year, addressing industry-specific applications in Automotive, CleanTech and Defense sectors. You will hear major manufacturers, leading nanotechnology product developers, and industry experts share product enhancements, insight on current market demands, commercialization opportunities, and much more.  It’s all about nanotechnology applications today — not years into the future.

Open Innovator’s Toolkit

What advantages lead major corporations to look for their innovations outside the organization? How can you benefit from the revolutionary strategies of open innovation? Find out when you join your colleagues in technology acquisition and licensing at yet2.com’s ninth Executive Briefing, held this year in Boston at the Hyatt Harborside Hotel, November 4-6. Our topic is Accelerating Innovation: The Open Innovator’s Toolkit. As always, our speakers are thought-leaders, decision-makers, and practitioners who are doing it well. They’ll deliver specific suggestions to make your technology acquisition or licensing efforts even more successful. Recent conferences have averaged 140–150 leaders representing 100+ global corporations from Asia, Europe, and North America.

Call for Source Code for Biology and Medicine

Dear Colleague,

We would like to invite you to submit your next manuscript to Source Code for Biology and Medicine.

Source Code for Biology and Medicine is an open access, peer-reviewed online journal published by BioMed Central. It covers source code employed over a wide range of applications in biology and medicine. The journal is advised by an expert Editorial Board.

Thanks to Source Code for Biology and Medicine's open access policy, all articles published in the journal are freely accessible online. Articles published in Source Code for Biology and Medicine are highly visible and read by a wide audience. Two of the most accessed articles published in the journal since its launch are:

Accesses 4166		Software review Gbrowse Moby: a Web-based browser for BioMoby Services Mark Wilkinson Source Code for Biology and Medicine 2006, 1:4 (24 October 2006) [Abstract] [Full Text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Accesses 2028		Research A traveling salesman approach for predicting protein functions Olin Johnson, Jing Liu Source Code for Biology and Medicine 2006, 1:3 (12 October 2006) [Abstract] [Full Text] [PDF] [PubMed] [Related articles]

To keep up to date with the latest articles, why not register to receive article alerts when new research is published?

Submit your research to Source Code for Biology and Medicine and take advantage of an efficient online submission process, a rapid, high quality peer-review service, and immediate publication upon acceptance. There are no color charges and no limits on the number of figures or embedded movies.

The published version of your article will be immediately placed in PubMed Central and other freely accessible full-text repositories. This complies with the NIH Public Access Policy and the Wellcome Trust Open Access Policy.

To enable the journal to make all of its content open access, Source Code for Biology and Medicine will levy an article-processing charge for each manuscript accepted after peer review (payable on acceptance).

Please submit your manuscript via our online submission system. For more information about the journal, contact peterson.leif@ieee.org or visit our instructions for authors.

Yours sincerely,

Emmanuel Ifeachor and Leif Peterson
Editors-in-Chief, Source Code for Biology and Medicine

Editors-in-Chief Emmanuel Ifeachor (United Kingdom) Leif Peterson (United States) Editorial Board Generoso Bevilacqua (Italy) Elia Biganzoli (Italy) Ramón Cacabelos (Spain) Xue-wen Chen (United States) Matthew Coleman (United States) Anne Denton (United States) Jose Fonseca (Portugal) Paolo Frasconi (Italy) Jonathan Garibaldi (United Kingdom) Owen Hoffman (United States) Jung-chang Huang (United States) Vasily Leonov (Russian Federation) Paulo Lisboa (United Kingdom) Francesco Masulli (Italy) Rita Noumeir (Canada) Lucila Ohno-Machado (United States) Silvano Paoli (Italy) Giovanni Parmigiani (United States) Ioannis Pitas (Greece) Edward Sarkisyan-Grinbaum (Switzerland) Scott Smith (United States) Roberto Tagliaferri (Italy) Manuel Ujaldon (Spain) Staal Vinterbo (United States) Michalis Zervakis (Greece)

CHI's 3rd Annual Bridging Pharma and IT - Leveraging Information Technology to Improve Productivity

September 30 - October 2, 2007  |  Hyatt Haborside  |  Boston, MA

Bridging Pharma and IT Conference is the only multi-track meeting to feature case studies of IT/Science paired discussions that provide insights into cross-domain partnering with an organization's end users and IT.

Keynote Presentations:

Doubling IT Innovation Spending: Laying the Foundation for IT-Enabled Business Process, Supply Chain, and Service Innovation in the Pharmaceutical Industry
Chris Asakiewicz, Ph.D., Affiliate Professor of Information Management, Stevens Institute of Technology, Wesley J. Howe School of Technology Management; former Vice President, Global Business Technology, Pfizer Global Pharmaceutical Division

Bridging Diagnostics Technologies with Pharma and Biotech
Tim Jaeger, Ph.D., M.B.A. Head of Medical and Scientific Affairs, Diagnostics Division, F Hoffmann La Roche AG

Creating the IT Infrastructure to Enable Adaptive Clinical Development
Jerald S. Schindler, Dr.P.H., Vice President, Late Stage Clinical Development Statistics, Merck & Co.

Lessons Learned: Challenges Faced in Sharing Information Across the Organization (Panel)
Marc Wine, MHA, Health Systems Analyst; Adjunct Professor Health Services Management and Leadership Department, The George Washington University   

Donald T. Mon, Ph.D., Vice President, Practice Leadership, American Health Information Management Association (AHIMA)

Mitchell Weisberg, Senior Principal, Hewlett Packard

6 Joint Case Studies From End Users & IT Executives

1.) Making the Most of Limited Resources: Creation of a Merckwide Biologics Database - Merck & Co., Inc.

2.) Developing a Knowledge Discovery Platform for Collaborative Research in Gastric Cancer - Singapore General Hospital & Nanyang Polytechnic

3.) Advancing Upload and Storage of Assay Data - Johnson & Johnson

4.) An Integrated Desktop Computing Environment for Chemists - Pfizer, Inc.

5.) IT Support for the Clinical Use of Genetics and Genomics - Could the Infrastructure in Place Today Be Strengthened through Collaborations with Pharma IT Departments? - Harvard Partners Center for Genetics & Genomics

6.) Are We Playing Dice With Informatics Projects? - Centocor R&D, Inc.

and More!!

Additional Presentations Include:

Developing of Enabling Informatics Technology in Support of the Development of Drug Candidates
Julie Hughes, Global Biologics Business IT Lead, Pfizer Global Research & Development

Building a Seamless Service - Implementing an SOA-Based Global Compound Sourcing Tool for Chemists
Mike Rippin, Ph.D., Director, Operations, Tessella, Inc.
Customer Co-Presenter TBD

One Company ~ 2 Worlds: Bridging Discovery and Development Information
Peter F. Thadeio, Research Porfolio Analyst, Pfizer Global R&D Groton Labs 

Using Biological Sequence Search to Validate Research Decisions
Kamalakar Gulukota, Ph.D., Senior Director, Content Development, GenomeQuest

Practical Applications of Modeling and Simulation in Clinical Studies
Dongzhou J. Liu, Ph.D., M.S., M.B.A., Principal Investigator, FRI New York

Application of Translational Informatics in Tailored Therapeutics
Susie Stephens, Ph.D., Research Scientist, Eli Lilly & Company

Brochure
Hotel
Register
Website

Howard R. Asher on the Convergence of IT and Life Sciences, Hypothetical Wireless Appliance

The Rady School of Management of the University of California, San Diego hosed the Second Annual Biotechnology Demystified Program to Teach the Science of Biotech to Business Professionals

Howard Asher, President and CEO of Global Life Sciences, Inc. presented on Technology Convergence: …the Role of IT in Life Sciences and Hypothetical Wireless Appliance.

Climate Savers Computing Initiative

<ed.note>In the meantime, of course, builders and computer vendors can begin deploying geothermal heat exchanger driven data centers. And we might all support the use of biosand water filters (portable potable) so there will actually be someone around to use those computers.</ed.note>

Believe it or not, the average desktop PC wastes nearly half the power delivered to it. Half! This wasted electricity unnecessarily increases the cost of powering a computer, and it also increases the emission of greenhouse gases. Improving the energy efficiency of computers is a cost-effective way to reduce electricity consumption and the emission of greenhouse gases that contribute to climate change. The Climate Savers Computing Initiative brings together industry, consumers and conservation organizations to significantly increase the energy efficiency of computers and servers.

Pharmaceutical Technology Annual Conference, July 24 - 26, 2007, Philadelphia, PA

FDA KEYNOTE ADDRESS:
FDA's Pharmaceutical Quality Assessment in the 21st Century - A Modern Risk-Based Approach Moheb Nasr, Ph.D., Director, Office of New Drug Quality Assessment, CDER, FDA

Pharmaceutical Technology magazine, the premier leader in cutting-edge information for the pharmaceutical industry, presents a case study driven conference orchestrated by an advisory board of highly respected experts. With R&D costs reaching astronomical levels in recent years, no one from a research scientist in an analytical lab to a QA manager in a  manufacturing facility can afford to ignore the cost savings associated with achieving process excellence across the entire spectrum of drug development.

"It is almost like one stop shopping to anyone having to deal with Quality, become a Lean manufacturing machine,and look for new Technology that will help them get there..."

Jack R. Hoblitzell, Ph.D., Director, Formulations Development, Banner Pharmacaps

OPTIMIZE PROCESS EXCELLENCE:
- 30+ Case Studies and Presentations from FDA, Pfizer, Wyeth, Merck, AstraZeneca, Novartis, Schering-Plough, Boehringer Ingelheim, Bristol-Myers Squibb, and more

- Lean Design and Development Applications on ALL levels from R&D through Manufacturing including Six Sigma, Validation, Formulation Development, Clinical Supply Manufacturing, Pharmaceutical Processes, and Manufacturing Product Lines

- Pharmaceutical Quality Initiatives Quality by Design (QbD), ICH Q8, ICH Q9, Quality Systems, Process Analytical Technology (PAT), Design of Experiments (DOE), and Risk Assessment

- Cutting Edge Technology PAT, Ultra Performance Liquid Chromatography (UPLC), ScanRDI, Laser Induced Breakdown Technology (LIBS), Data Automation, Mathematical Modeling, and Process Transfer

REGISTRATION:
Sign up today, and maximize the best price option for this conference.
Please visit or call toll free 1-888-524-9922 or 218-740-7028 (int'l only).

10% Off of Conference Registration For Bioinformatics.Org Members Only: Please use priority code BIODS when registering.

Download the Conference Agenda

Biomarker Discovery Summit: Bridging the Silos in Biomarker Discovery and Validation, September 17-19, 2007, Philadelphia

www.BiomarkerDiscoverySummit.com

Track 1: Third Annual Genomic Biomarkers
Track 2: Fifth Annual Protein Biomarkers
Track 3: Eighth Annual Metabolic Biomarkers
Track 4: Third Annual Toxicity Biomarkers

Event features:
Network with 400+ delegates
Get access to FOUR established meetings under one roof
Choose from a greater selection of pre-conference workshops and tutorials
Learn about new tools at the expanded exhibit hall and new technology showcases
Experience a Biomarker Series event, now in its 5th year
Featured Speakers:

William B. Mattes, Ph.D., Director of Toxicology, The Critical Path Institute
Carrie Brodmerkel, Ph.D., Assistant Director, Clinical Pharmacology and Experimental Medicine, Centocor R&D
Hans Winkler, Ph.D., Senior Director, Functional Genomics, Johnson and Johnson Pharmaceutical R&D
Koustubh Ranade, Ph.D., Director, Pharmacogenomics & Human Genetics, Pharmaceutical Research Institute, Bristol-Myers Squibb
Emanuel F. Petricoin, Ph.D., Co-Director, Center for Applied Proteomics and Molecular Medicine; and Professor of Life Sciences, George Mason University
Sunil Kadam, Ph.D., Research Scientist Medical Genomics, Eli Lilly & Co
Stephen Furlong, Ph.D., Director, Discovery Medicine, AstraZeneca
Viswanath Devanarayan, Ph.D., Associate Director, Experimental Medicine & Biomarkers, Merck Research Labs
Jean Lee, Ph.D., Scientific Director, PKDM, Amgen Inc.
Frances Clemo, Ph.D., Director, Safety Sciences, Pfizer Global R&D
Weida Tong, Ph.D., Director, Center for Toxicoinformatics, National Center for Toxicological Research, FDA
Jinzhi Chen, Ph.D., Head Genetics/Genomics, Proteomics/Biomarker Discovery, Roche Palo Alto
John J. Sninsky, Ph.D., Vice President, Discovery Research, Celera Diagnostics
Qiuwei Xu, Ph.D., Merck Research Laboratories
Jill M. Kolesar, Pharm.D., Associate Professor of Pharmacy, University of Wisconsin-Madison
Mark E. Curran, Ph.D., Director, Biomarker Biology, Clinical Discovery Technologies, Bristol-Myers Squibb
Glenn A. Miller, Ph.D., Genzyme Analytical Services
Richard Beger, Ph.D., Branch Chief, Center for Metabolomics, Division of Systems Toxicology, National Center for Toxicological Research
William Hancock, Ph.D., Bradstreet Chair, Barnett Institute, and Department of Chemistry and Chemical Biology, Northeastern University
Kevin Wang, Ph.D., Director, Center for Neuroproteomics and Biomarkers Research, McKnight Brain Institute, University of Florida
George Calin, Ph.D., Assistant Professor, Molecular Virology, Immunology and Molecular Genetics, Ohio State University
Daniel Raftery, Ph.D., Professor of Chemistry, Department of Chemistry, Purdue University
Vladimir Tolstikov, Ph.D., Director, Metabolomics Core, UC Davis Genome Center
Natalie J. Serkova, Ph.D., Associate Professor of Anesthesiology and Radiology, Cancer Center MRI/MRS Core, University of Colorado Health Sciences Center

For more information, please contact: Julia Boguslavsky, E-mail: juliab@healthtech.com

For sponsorship information, please contact: Angela Parsons, E-mail: aparsons@healthtech.com Phone: 781-972-5467

Alternative Splicing: Beyond Genes to Proteins June 21-22, San Francisco

Program here.

Bioinformatics.org Perl and R courses, May 28-June 15

1. PERL FOR BIOLOGISTS, LEVEL 1 May 28-June 1, 2007

DESCRIPTION:
This course is designed to help researchers learn how to use the scripting language Perl to automate certain tasks in their research. The topics taught involve laboratory scenarios and datasets, and include installing and running simple Perl programs; variables (scalars, arrays); printing; variable interpolation; string operations; mathematical, conditional and logical operators; file input/output; loops (if-then-else, for, while); list operations; regular expressions; and functions. Students will be assigned a project at the end of the week.

SCHEDULE:
Each lecture will start at 15:30 UTC (11:30 AM US EDT) and last 45 to 90 minutes, depending on the topics covered.

FOR MORE INFORMATION: http://edu.bioinformatics.org/CG

2. R FOR BIOLOGISTS, LEVEL 1  May 28-June 1, 2007

DESCRIPTION:
This course is designed to help researchers learn how to use the statistical scripting language R for data analysis. The topics taught involve laboratory scenarios and datasets, and include installing and running R; understanding the R interactive environment; creating, storing and manipulating R data objects; reading data from files; applying built-in functions on data; for-loops, if-then-else statements; scripts; functions; and packages. Students will be assigned a project at the end of the week.

SCHEDULE:
Each lecture will start at 17:00 UTC (1:00 PM US EDT) and last 45 to 90 minutes, depending on the topics covered.

FOR MORE INFORMATION:
To find out more information on the course, including the registration process, please see the course schedule page: http://edu.bioinformatics.org/CT

3. PERL FOR BIOLOGISTS, LEVEL 2  June 11-15, 2007

DESCRIPTION:
This course is designed to help researchers understand the scripting language Perl. It is a continuation of Perl for Biologists, Level 1 and covers advanced topics such as scripting with BioPerl, the Perl DBI and DBD for connecting to databases, high-throughput BLAST analysis, and writing multi-function scripts and converting them into Perl modules and packages.

SCHEDULE:
Each lecture will start at 15:30 UTC (11:30 AM US EDT) and last 45 to 90 minutes, depending on the topics covered.

FOR MORE INFORMATION:
To find out more information on the course, including the registration process, please see the course schedule page: http://edu.bioinformatics.org/GA

4. R FOR BIOLOGISTS, LEVEL 2  June 11-15, 2007

DESCRIPTION:
This course is designed to help researchers understand the data analysis/visualization language R. It is a continuation of R for Biologists, Level 1 and covers advanced topics such as working with Affymetrix CEL files and data analysis with the Bioconductor packages.

SCHEDULE:
Each lecture will start at 17:00 UTC (1:00 PM US EDT) and last 45 to 90 minutes, depending on the topics covered.

FOR MORE INFORMATION:
To find out more information on the course, including the registration process, please see the course schedule page: http://edu.bioinformatics.org/GC

Latest Life Sciences Information Technology (LSIT) Global Institute Minute

here.

Oh Sure, Everyone SAYS they want Open Source Healthcare Solutions...

<ed.note>... but when it comes to ponying up the dough, Eishay notes:</ed.note>

I thought that it’s expected of the applications to be commercial or commercial ready. Doesn't IHE expect the vendor that subscribes to the Connectathon to be serious about taking the tested application to the market as product? Won't it violate the spirit of the Connectathon if I'll hack up some panels that trigger the underlying actors without it look remotely like something a physician will ever consider using? Actually it will be much simpler to run them from the command line :-)

Coming from IBM research we have some serious problems sponsoring this huge code investment, and vendor integration+education. To most of the vendors we serve as a major IHE support, explaining how to do the MESA tests, and how to "think IHE Secured Node" etc. Note that we are implementing seven actors and supporting dozen vendors, we expect the number of vendors using OHF to more then double by next year.

This year IBM supported the open source openEMR application participation fees. We will probably not be able to do it next year. I know of open source applications that wish to go to the '08 Connectathon (openEMR, Mirth, Tolven, MirrorMed, and more are coming). They have lots of motivation that comes with considerable barriers in the shape of travel expenses plus the investment in integration, implementation, and passing the MESA tests. From talks with them I understand that the 8K$ registration fees is something they will not be able to swallow, and I assume that it will prevent them from participating in the event.

I see it as a big miss to IHE since these end user applications have real users in the market. Each of them have a unique characteristic that can display more innovative ways of integrating IHE in the market. For example the Tolven's PDA PHR application with its personal medical devices integration, and Mirth's healthcare messaging integration server.

American Health Information Community News

Monya's "Federal Workgroup Releases Guidelines for Verifying Patient Identities" here. Health Management Technology reports in "AHIC Forms Group to Consider Standards for Incorporating Genetic Data in EMRs" that at "the behest of HHS Secretary Mike Leavitt, the American Health Information Community formed a work group to consider standards by which genomic data could be included in EMRs. "

Optics Tests For Early Alzheimer's Diagnosis Make Significant Advances

Photonics Online

Washington — Providing an update on progress and new findings on his optical tests for the early detection of Alzheimer’s disease, Lee Goldstein of Brigham and Women’s Hospital and Harvard Medical School described dramatic new developments in the technology during a plenary talk at Frontiers in Optics, the annual meeting of the Optical Society of America (OSA) in Rochester, NY.

At the plenary talk, Goldstein presented “proof of concept” evidence obtained in mice that the tests can detect early molecular signs of the disease in the eye even before Alzheimer’s pathology is present in the brain. This achievement raises hopes for detecting the disease at its earliest stages and slowing the progression of the disease to a crawl.

Goldstein envisions that the tests could become part of a suite of “universal early screening technologies” that would be a routine part of an annual physical exam for people starting in middle age. With the tests, envisioned to be relatively inexpensive, physicians would be able to monitor patients year to year for any signs that the disease is present and progressing. The goal, according to Goldstein, is to catch the disease early in its course when treatment is likely to be most effective.

Biomedical Ontology in Action - [ Update: Accepted Papers ]

The accepted papers are listed here.

November 8, 2006, Baltimore, Maryland, USA

http://www.imbi.uni-freiburg.de/medinf/kr-med-2006

Workshop organized bythe National Center for Ontology Research (NCOR) and the Working Group on Formal (Bio-)Medical Knowledge Representation of the American Medical Informatics Association (AMIA)

Collocated with FOIS 2006

In recent years, a good deal of attention has been paid to the sorts of criteria that an ontology must satisfy if it is to ensure trueinformation integration and automatic reasoning across large-scale knowledge sources. Formal ontology is now an established field of research with conferences such as FOIS and organizations such as NCOR.The biomedical domain is at the leading edge of ontology research, as illustrated by the recent creation of the National Center for Biomedical Ontology, a NIH Roadmap center.

Standing on the foundations of biomedical ontologies are the many applications supported by these ontologies. For example, in health care, ontologies are an important component of an interoperable health information technology infrastructure. In biology, ontologies have become essential for annotating the literature and integrating the multiple, heterogeneous knowledge bases resulting from the analysis of high-throughput experiments.

This workshop aims at bringing together researchers from a broad range of fields that are related to formal ontology and medical informatics. The goal is to show how current research can be brought tobear on the practical problems associated with the development ofapplications supported by these ontologies, i.e., to show biomedical ontology "in action".

The scope of KR-MED 2006 includes the following areas:

Biomedical ontologies and electronic health records (EHRs)

Semantic Web applications in healthcare and life sciences

Use of ontologies in knowledge discovery, text analysis and data mining

Biomedical ontology evaluation

Temporal, spatial and causal knowledge reasoning in biomedical systems

Knowledge representation, acquisition, validation, visualization and maintenance in biomedical systems

Applications of knowledge representation languages, description logics for biomedical systems

Formal approaches to large biomedical controlled terminologies and vocabularies

Important dates

Paper submissions due: July 7, 2006

Notification of paper acceptance: August 18, 2006

Final paper deadline: September 15, 2006

Workshop: November 8, 2006

Applied Biosystems Launches Software Development Community

which hopes to foster interoperability.

Folding@Home PS3 client announced

PS3 client announced today. Today in Germany, Sony demoed their Folding@Home client for the PS3. For more details, check out our PS3 FAQ. Using the Cell processor of the PS3, we should be able to do more folding than what one could do on a PC. Also, since the PS3 has a powerful GPU, the PS3 client will offer real time visualization for the first time. Check out the PS3 FAQ for some early movies of that. The PS3 client and GPU client are together part of our new broader goals to push Folding@Home to the next stage, reaching calculations on the petaflop to 10 petaflop scale. We have some preliminary details on our Folding@Home Petaflop Initiative (FPI). We will release more details on all of this as the new software rolls out. We are beta testing the ATI GPU client software internally at the moment and will likely announce an open beta in four to five weeks (end of September).

nanoTX'06 September 26-28

Sean Murdock, Executive Director, the NanoBusiness Alliance announces that the NanoBusiness Alliance has joined the list of major organizations sponsoring , a world class nanotechnology conference and trade expo, to be held at the Dallas Convention Center. The event is international in scope, with 160 speakers from 30 countries expected, but the strong participation of Texas's semiconductor and microelectronics industries alone would make this event worthwhile. The theme of the event is "The Promise of Tomorrow: The Business of Nanotechnology". H. Ross Perot of Dallas, internationally renowned business leader and two-time Presidential candidate, will deliver the opening remarks on September 27. The other key highlight is the Nobel Laureates Legends Reception (dedicated to the memory of the late Jack Kilby and Rick Smalley) which will feature six Nobel Laureates. The event is hosted by the Texas Nanotechnology Initiative, which has done a fantastic job bringing together Texas's universities, start-ups and Fortune 500 companies for this event. For more information, please visit www.nanotx.biz. Trends here.

OpenWetWare

OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, we hope that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world.

Bioclipse 0.9.9 released ( A visual framework for chemo- and bioinformatics using the Eclipse Rich Client Platform )

Friday, 28 July 2006 by Ola Spjuth

Bioclipse 0.9.9 has been released as the last pre-1.0 version. The download is available from Sourceforge [1]. We would appreciate everyone to test this version and report bugs to the sourceforge project site [2]. Version 1.0 is scheduled for release on August 11th.
Bioclipse homepage: www.bioclipse.net

[1] Bioclipse downloads - http://sourceforge.net/project/showfiles.php?group_id=150681
[2] Bioclipse bug reports - http://sourceforge.net/tracker/?group_id=150681&atid=778609

See also here.

College Launches Research Facility With Real-Time Connectivity

6/29/2006 Walters-Storyk Design Group

The Gene Center at Hunter College in New York, NY, recently opened a new Internet2 Distance Research & Learning Facility. Designed by the Walters-Storyk Design Group, the new facility is driven by high-speed Internet2 transmission and promotes real-time collaborative experimentation and teaching projects within the international gene research community.

“Internet2 speed, reliability, and clarity will enable us to virtually share the same laboratory with colleagues at over 200 research institutions and universities in this country and with similarly equipped institutions around the world,” said Robert Dottin, Ph.D., director of the Gene Center for the Study of Gene Structure & Function.

The facility is comprised of two rooms, which include soundproof doors, acoustic ceiling treatments, and dual interior windows to create a sound lock. WSDG also incorporated a sound curtain to block any nearby street noise leakage. Equipment includes a flat panel monitor, projectors, a video camera for robotic tracking, wireless microphones, and retractable projection screens. The entire complex can be controlled by a single Crestron touch screen mounted on the lectern in Conference A or via a computer in the adjacent support office.

A mobile studio has also been designed to provide full AV and Internet connectivity to individual labs within the Hunter College Gene Center. This studio can monitor real-time experiments ranging from behavioral studies of live lab mice to collaborative microscopy, and transmit live coverage to research institutions and universities participating in the Internet2 network.

Unified Medical Language System

The purpose of the U.S. National Library of Medicine's Unified Medical Language System  ® (UMLS) is to facilitate the development of computer systems that behave as if they "understand" the meaning of the language of biomedicine and health. To that end, NLM produces and distributes the UMLS Knowledge Sources (databases) and associated software tools (programs) for use by system developers in building or enhancing electronic information systems that create, process, retrieve, integrate, and/or aggregate biomedical and health data and information, as well as in informatics research. By design, the UMLS Knowledge Sources are multi-purpose. They are not optimized for particular applications, but can be applied in systems that perform a range of functions involving one or more types of information, e.g., patient records, scientific literature, guidelines, and public health data. The associated UMLS software tools assist developers in customizing or using the UMLS Knowledge Sources for particular purposes. The lexical tools work more effectively in combination with the UMLS Knowledge Sources, but can also be used independently.

There are three UMLS Knowledge Sources: the Metathesaurus ®, the Semantic Network, and the SPECIALIST Lexicon. They are distributed with flexible lexical tools and the MetamorphoSys install and customization program.

MIT Scientists Ask Biologists to Imitate Engineers

June 21, 2006 By M.L. Baker, Ziff Davis Internet

Biotechnology could enjoy more of the efficiency and innovation of high technology, say a group of experts working at the intersection of computation and biology. But first, researchers have to think less like scientists and more like engineers.

By inserting new collections of genes into bacteria, teams of "biohackers" can make microorganisms do nifty tricks: reproduce black and white photographs, form a ring oscillator, work as an etch-a-sketch under a ultraviolet pen, even detect whether coffee is decaf, regular or espresso.

But biologists can't take a trick invented by one lab and combine it with tricks invented by someone else.

... In 2003, [MIT professor Drew] Endy and others set up the Standard Registry of Biological Parts. The idea was to get biologists to write interoperable plug-ins in DNA code. These plug-ins are described in an online database and stored in a freezer at MIT.

All researchers have to do is follow a set of assembly rules when designing their genetic gizmos, essentially making sure that the wiring required for one won't short-circuit another. That approach is standard operating procedure for many computer engineers.

The 2006 Venture Forum

Attendees will have the opportunity to access one of the nation's largest technology pipelines from federal agencies, universities, and a global network, including:

    * The National Institutes of Health (NIH)
    * The National Institute of Standards and Technology's Advanced Technology Program (NIST's ATP)
    * Defense Advanced Research Projects Agency (DARPA)
    * Top Universities & Research Institutions such as: UCLA, USC, UCSB, UCI, California Pacific Medical Center, MIT, Stanford,   and the Illinois Institute of Technology. 
    * Global Innovators from Australia, Canada, Hong Kong, Italy, Korea and Taiwan. 
    * And other carefully selected & mentored companies from around the U.S.

For over 11 years, Larta Institute has successfully showcased the nation's top innovative & investment-worthy technologies. Companies that present at the Venture Forum are rigorously reviewed & mentored by Larta's elite panel of investors and subject matter experts.

On Wednesday, June 28th and Thursday, June 29th, hundreds of venture capitalists, angels, corporate investors and leading service providers from across the globe will gather in Silicon Valley to discover the most groundbreaking seed and early-stage investment opportunities and to engage with expert panels on innovation.

Click here to read more about the 2006 Venture Forum

International Congress on Nanobiotechnology & Nanomedicine (NanoBio2006)

June 19-21, 2006

Open Development Initiative (ODI), Center for Bioinformatics, National Cancer Institute

The NCICB Open Development Initiative (ODI) is an exciting opportunity for members of the bioinformatics community to extend the work being done by NCICB staff and contractors. Are you an innovator, a pioneer? Do you find yourself wondering "why not" versus "why", "what if" versus "what" and "let’s do it" versus "when will they"? Do you long to participate in the development and deployment of leading edge analytic and knowledge tools, designed to help solve difficult and complex problems? This is the place for you!

The NCICB ODI offers the opportunity to get involved in shaping the next frontier for NCICB software development as we pursue our vision of rapidly expanding the suite of applications and infrastructure. We can’t do it alone. We don’t want to do it alone. We need your creative talents, your unrestrained enthusiasm and ideas to enhance and grow the next generation of bioinformatics tools. Over the remainder of this year this initiative will mature, now is the time to get in on the ground floor!

Source Code for Biology and Medicine

A brand new journal, Source Code for Biology and Medicine, soon to be launched by BioMed Central.

Source Code for Biology and Medicine is an open access, peer-reviewed online journal that encompasses all aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining.

Source Code for Biology and Medicine offers rapid, high quality peer-review, overseen by its distinguished international Editorial Board, an efficient online submission process, no colour charges or limits on the number of figures, and immediate publication upon acceptance. The published version of your article will be immediately placed in PubMed Central and other freely accessible full-text repositories, making it highly visible to fellow researchers and a general audience worldwide. This complies with the NIH Public Access Policy and the Wellcome Trust Open Access Policy.

To enable the journal to make all of its content open access, Source Code for Biology and Medicine will levy an article-processing charge for each manuscript accepted after peer review (payable on acceptance).

Source Code for Biology and Medicine is now accepting submissions. Submit your manuscript via our online submission system. For more information about the journal, contact peterson.leif@ieee.org or visit our temporary information page.

Yours sincerely

Emmanuel Ifeachor and Leif Peterson

The Editors-in-Chief, Source Code for Biology and Medicine

Editors-in-Chief: Emmanuel Ifeachor (UK) and Leif Peterson (United States)

Editorial Board: Generoso Bevilacqua (Italy); Elia Biganzoli (Italy); Ramón Cacabelos (Spain); Xue-wen Chen (United States); Matthew Coleman (United States); Anne Denton (United States); Jose Fonseca (Portugal); Paolo Fransconi (Italy); Jonathan Garibaldi (UK); Owen Hoffman (United States); Jung-chang Huang (United States); Vasily Leonov (Russian Federation); Paulo Lisboa (UK); Francesco Masulli (Italy); Rita Noumeir (Canada); Lucila Ohno-Machado (United States); Silvano Paoli (Italy); Giovanni Parmigiani (United States); Ioannis Pitas (Greece); Edward Sarkisyan-Grinbaum (Switzerland); Scott Smith (United States); Roberto Tagliaferri (Italy); Manuel Ujaldon (Spain); Staal Vinterbo (United States); Michalis Zervakis (Greece).

Rosetta@home 7th Biennial Critical Assessment of Techniques for Protein Structure Prediction Experiment from May 10th until August 1st

Rosetta@home is working to develop software to accurately predict the folding structure of proteins, which is a key function in developing cures for diseases such as AIDS, cancer, and Alzheimer's. The Rosetta software is used by other scientists and distributed computing projects. Any improvement we can make in this project will benefit other scientists and projects as well.

Cutting-Edge Research with an all new Application package

The Rosetta@home science application has improved greatly in recent weeks. We now have "smarter" software and new techniques which help find the best structures faster. We have also released a number of new features:

• Work unit runtimes based on preference setting can minimize your internet use.
• More frequent saves (checkpointing), means more science output and more credits for you and your team.
• The "Watchdog" keeps work flowing by ending work units that appear stuck or hung.
• All work units will receive credit even if they return late or with an error result.

All these improvements guarantee a problem-free and most useful contribution of your valuable computer time.

CASP7 is here - Be part of the competition and the winning team!

There are many science teams working on protein studies, and every 2 years they conduct a contest of sorts, to define the current state-of-the-art. Now the 2006 event is underway, and you can help. CASP will present proteins no one has ever seen before and ask the research teams to give their best structure predictions for this computationally intense problem. We are very hopeful the improved Rosetta software, now with the added power of distributed computing, will again find the most accurate predictions.

CASP7 runs from May 10th to August 1st. The more computing power we apply, the better the predictions become. Please be sure to run Rosetta@home, at least during the three month period of the competition. Read more about CASP7, and check for published results on the Rosetta@home website through the end of the year.

Be a part of the project team with new information and user recognition

A number of new informational features have been added to help you participate with the research team:

• "Dr. Baker's science journal" where the project's lead scientist posts regular updates and project news.
• Work Unit information describes the proteins and tests being performed for each work unit type.
• The Application Version Log explains new features and scientific improvements in the application.

The project staff is very responsive to questions and suggestions and is working to incorporate them into Rosetta application improvements.

What you can do to help

• If you discontinued Rosetta for any reason, please attach again and you will find the application improvements have resolved the problems many were having.
• Dedicate a greater resource share to Rosetta, at least during CASP7.
• Attach additional computers to the project.
• Contact your friends and teammates and help them learn more about Rosetta so they will want to crunch more too. Here is a simple explanation you might use.
• If you are a member of a team, please ask for more Rosetta processing time on your team message boards.

Take a look at "10 reasons why I support Rosetta@home and you should too."

Thank you for your past participation, and we hope you can provide additional support to Rosetta@home in the future.

Mark, Joachim, Gerry and the Rosetta@home volunteers

Life Sciences Information Technology (LSIT) Global Institute GIPedia, the encyclopedia of Good Informatics Practices, Launched

On April 25, 2006 LSIT held an “All Hands GIP Working Group” meeting to bring together many of the volunteers who are contributing content and user knowledge in our GIP Guidance Document.  As several of our out-of-US/state volunteers were unable to attend, LSIT would like to take this opportunity to update you all on the meeting and our progress to date.

Because of the progress we’ve made, this update is being sent you to reach out for your input.  We are ready to hear from you through our test Wiki “Sandbox” @ http://www.spincom.com/gipedia/ . Read on for more details.

We would like to extend a special thank you to John Kim, Paul Laskin, Bill Branan, and Laurence Dorazio for facilitating the meeting.

Highlights from the meeting included:

1. A recap of pertinent information from our initial meeting in January, including the importance of volunteers, Development Objectives for GIP and Document Management and Standards.

2. Overview of Document Production Tools:  Wiki, Microsoft Office, Groove

• a. We have embraced Wiki technology as a critical component of gathering key content from subject matter experts like you.  It is open and accessible and needs to be populated by your efforts.  (For a brief overview of the technology:  http://www.reference.com/browse/wiki/Wiki) From initial contributions to “GIPedia”, our encyclopedia of Good Informatics Practices, we will compile the best of the best, screen and vet for inclusion in GIP.  We have registered the domain name “GIPedia.org” as the eventual site for this GIP wiki, and we will soon send out an announcement when it is activated.
• b. LSIT’s Groove workspaces support our Project Lead and Management volunteers to oversee quality and accuracy.  Groove will be the ”place” where we conduct the internal edit and review process.  After a rigorous internal review that will include key organizations like the FDA & GAMP, GIP will be ready for peer/public review.  These requests for review will be published in our newsletter, the LSIT Minute (http://www.lsit.org/lsit_minute/).  If you know of someone who would appreciate receiving the newsletter, please let me know.

3. An overview of the structured Working Groups (http://www.lsit.org/initiatives/workinggroups.php that represent sections of the GIP Guidance Document (See table of contents: http://www.lsit.org/initiatives/gip-toc.php), and updates on their activities.

• c. The Security Chapter of GIP is just about written and will be ready for its first review cycle in a couple of weeks.
• d. The Validation and Verification Working Group will be led by Mira Milovancev, who has recruited six volunteers from the life science community.  The outline for this chapter has already had a first review and feedback by the FDA.
• e. The Infrastructure Group will be jointly chaired by Tony Pietsch and Beth Kennedy.  Infrastructure is a critical component to the development of GIP and we need volunteers to address some of the systems, hardware and structure issues.  Please contact us if you can help.

Thank you one and all for your incredible support and commitment to effecting change for the good of this industry.

Sincerely,

Anette Asher
Executive Director
Life Science Information Technology Global Institute
858-759-4750
http://www.lsit.org

TN Broadband Stimulus Program

Kevin Bittorie, Director of Programs & Communications, Nashville Technology Council Program Announcements

Broadband access is increasingly becoming a key question businesses are asking when looking at relocating to Middle Tennessee.  The Tennessee Department of Economic Development has developed a brief survey to support the Tennessee Broadband Stimulus Program.

There is a Residential Survey to be completed by everyone and a separate Business Survey to be completed by the appropriate executives.  The link to the business survey is also included on the last page of the residential survey.

Eric Cromwell and his staff are trying to reach as many people across the state as possible with this survey - the more feedback we receive the more beneficial and effective our efforts will be - so we thank you for and value your input.  Please make sure to distribute this message to the appropriate people in your communities.

Open Bioinformatics Foundation

The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.

The foundation grew out of the volunteer projects Bioperl, BioJava and Biopython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from the member projects, there is clear commonality of direction and purpose. Occasionally the O|B|F directors may make announcements about our direction or purpose (a recent one was on the licensing of academic software) when the board feels there is a need to clarify matters, but in general we prefer to remain simply the administrative support organization for our member projects. Project Wiki here.

Managing the Clinical Data Flood

Patrick McGee, Senior Editor, Drug Discovery & Development

...many companies will also choose to use tools such as Northrop Grumman's GTM, which features an integrated planning and monitoring environment that simulates all aspects of a clinical trial. It supports research study start-up activities, site initiation, patient enrollment and monitoring, data collection throughout the trial, and analysis of project metrics and results. Other features include real-time reporting and tracking, automated alerts and notifications of tasks, and the ability to search for, identify, and respond to key data points.

Light says GTM is easy to bring online and begin using. "It's not something where you have to go in and build your business process into it and all your terminology. The application comes ready to be able to use interfaces to put in all of that information, and it will ripple through the rest of the system seamlessly." She says another differentiating factor is how it handles offline processing. When companies send personnel to monitor a clinical investigative site, they don't always have an Internet connection and they often don't have much room to work in. "Being able to use information and process it offline, again without having to put it on paper and give it to someone else to enter into the system, would be a key capability."

To do this, the GTM uses Microsoft Office's InfoPath, a program written in Extensible Markup Language (XML) that allows businesses to design and fill out electronic forms that can be easily shared and manipulated. "You don't need to have any type of Internet connection, but through XML we transfer information to and from the database with reconciliation rules, which again, from the user perspective, is something they don't need to know anything about. It just happens when they download things to get ready to go out to the site and when they plug back in at the end of the night," Light says.

Researchers Combine Tiny Nanotubes And Antibodies To Detect Cancer

12/13/2005 photonicsonline.com

By coating the surfaces of tiny carbon nanotubes with monoclonal antibodies, biochemists and engineers at Jefferson Medical College and the University of Delaware have teamed up to detect cancer cells in a tiny drop of water. The work is aimed at developing nanotube-based biosensors that can spot cancer cells circulating in the blood from a treated tumor that has returned or from a new cancer.

The researchers, led by Eric Wickstrom, Ph.D., professor of biochemistry and molecular biology at Jefferson Medical College of Thomas Jefferson University in Philadelphia and at the Kimmel Cancer Center at Jefferson, and Balaji Panchapakesan, Ph.D., assistant professor of electrical engineering at the University of Delaware in Newark, present their findings November 17, 2005 at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics in Philadelphia.

National Center for Biomedical Ontology Launched

Mark Musen announces:

As many of you know, part of the Roadmap initiative of the National Institutes of Health (http://nihroadmap.nih.gov/) includes major support for biomedical computation through, among other mechanisms, the creation of National Centers for Biomedical Computing (http://www.bisti.nih.gov/ncbc/index.cfm). The NIH just announced the three new National Centers to be created this year, and one of them will a "National Center for Biomedical Ontology" (see http://www.bioontology.org).

The National Center for Biomedical Ontology is being founded by a consortium that brings together the Protégé group at Stanford, the informatics team of the Gene Ontology Consortium centered at Berkeley, the informatics group at the Mayo Clinic responsible for the Common Terminology Services standard promoted by HL7, the ontology group in the Department of Philosophy at SUNY-Buffalo, and several other collaborating centers. Together, we will develop new technology for managing libraries of biomedical ontologies, for indexing, aligning, and annotating biomedical ontologies, and for facilitating peer review of online knowledge resources in both clinical medicine and the life sciences. We also plan to develop technology to help biologists to use ontologies, primarily in the area of annotating large data sets. We are planning outreach activities to help biomedical scientists in the development and refinement of ontologies in particular domains.

The NIH roadmap initiative includes set-aside funds to encourage investigators at other institutions to collaborate with the National Centers for Biomedical Computation (see http://grants.nih.gov/grants/guide/pa-files/PAR-05-063.html) This grant mechanism might provide a very tangible way to fund projects of importance to Ontolog.

The National Center for Biomedical Ontology, with its primary administrative site at Stanford, involves several investigators who also are involved in the National Center for Ontological Research (http://ncor.us), which has previously been announced on this forum. The two Centers have distinct missions, but should be extremely synergistic. The National Center for Biomedical Ontology is an NIH- funded entity with the primary aim of creating specific technologies to promote the management and application of ontologies in biomedicine. The National Center for Ontological Research is an umbrella organization that will be seeking funding from a variety of sources to promote the application of ontologies in a wide range of disciplines and to offer educational programs to encourage sound principles of ontology design.

We are extremely excited that the NIH has recognized the importance of ontologies in biomedical research through the funding of our new Center. It makes us feel that ontologies are almost becoming mainstream!

Drug Scientists Slow to Adopt Open Source

Sept. 8, 2005 By M.L. Baker, Ziff Davis Internet

A surge in open-source technology offers many businesses a potent combination of power and low cost, but the pharmaceutical industry remains well behind the curve.

That was the message at a session on data visualization and integration at a semiannual meeting of the nation's chemists in Washington last week.

No one thinks open source can fill everyone's software needs, but a "forceful" open-source community could create modules that bridge gaps in existing software designed for the pharmaceutical industry and help it become more efficient, said presenters. Yet so far, few are stepping up to the plate.

Interest in visualization software has surged in the pharmaceutical industry in the past couple years, but interest in open source has not, said Carol Rozwell, vice president of life sciences at consultancy Gartner Inc., who did not attend the session. However, she said, interest might pick up as the pharmaceutical industry sees IT more firmly integrated into drug discovery and development.

<ed.note>We just launched a "bio park" just south of Nashville. I've always hoped that folks with disabilities from the rural areas of tennessee would be able to plug into a broadband grid environment and be employable via "net-work". Just did this scholar.google.com search -- coupla hundred hits. Looks like there is some nascent interest out there...</ed.note>

An Emerging Industry Standard for Linking Genomic Sequences to Biological Function

New expanded release (2002) - BSML v3.1

Extensible Markup Languages describe data in a way that captures the semantics of encoded information, allowing more efficient access to information. BSML is an extensible language specification and container for bioinformatic data.

BSML encodes biological sequence information and includes graphical representations of biologically meaningful objects such as sequences, genes, electrophoresis gels, and multiple alignments.