Entries in "Biological Sciences" ( for this category only)

Coyotes Are Texting

The Akron Beacon Journal (December 29, 2010) reports that coyotes in northeast Ohio are "texting" their locations to researchers. Their collars are equipped with global positioning systems that text the locations to the research team consisting of people from several universities and park systems.

Kids Publish in Peer Reviewed Science Journal

Biology Letters has published a journal article by 8 to 10-year olds investigating how bumblebees see colors and patterns.

Future scientists in action!

See the Associated Press article for more information.

Mathematical Biology Now Covered by Biology Direct

Biology Direct considers original research articles, hypotheses, comments, discovery notes and reviews in selected subject areas, and will eventually cover the full spectrum of biology. Subject areas already launched include Genomics, Bioinformatics and Systems Biology, Immunology, and Mathematical Biology.

Andrei Yakovlev wrote an editorial that kicked off the new commitment to Mathematical Biology.

Modern mathematics offers a much richer arsenal of tools and ideas than those that are frequently employed to describe the enormous diversity of biological phenomena.

Midwest Biomedical Engineering Conference

The Case School of Engineering is hosting the Midwest Biomedical Engineering Conference on February 23. Online registration, abstract submission, and resume submission are now open. All abstracts and resumes must be submitted by February 9. For more information, go to http://www.mbecconference.org/.

From website:

MBEC 2007: "Showcasing the future of biomedical engineering"

The Midwest Biomedical Engineering Conference (MBEC) 2007 is designed to bring together students & practitioners of Biomedical Engineering and the Life Sciences for panel discussions, technical sessions, and informal extended exchange of ideas important to the future of Biomedical Engineering in the Midwest. Some conference highlights include:

  • Assisting participants in planning their academic and industrial careers
  • Introducing companies to the wealth of intellectual prowess rooted in the Midwest
  • Exposing participants to innovative research in biomedical engineering and allied areas
MBEC 2007 is hosted by Case Western Reserve University. All universities are welcome to attend.
[VIA: Case Daily - February 02, 2007]

Continue reading "Midwest Biomedical Engineering Conference"

Online Encyclopedia of Medical Images

Effective January 1st, the entire OhioLINK community has access to Images.MD.

Images.MD, the online encyclopedia of medical images, compiles more than 55,000 images from more than 90 collections ranging from allergy to urology, each accompanied by detailed and informative text contributed by more than 2,000 medical experts.

Members of OhioLink have free access to full-sized, high quality images in step with the latest developments in medicine. By filling out a simple registration form, you can also start your own image library, create PowerPoint® presentations of images in your library, and order customized CD-ROMs of your favorite slides.

New Purchase - Encyclopedia of Biostatistics Online

The Encyclopedia of Biostatistics (2nd Ed.) offers the definitive reference to support the development and use of statistical methods for addressing the problems and critical issues that confront scientists, practitioners and policy makers engaged in the life and medical sciences. With the growing importance and application of biostatistics, reflected in the increasing number of statisticians employed in the pharmaceutical industry, healthcare sector and medical schools, this new edition will find widespread application in basic medical science; the planning, financing and distribution of health care; and the measurement of health care status and progress in the population.

The Encyclopedia now includes many contributions that focus on the rapid growth of bioinformatics and its pivotal role in studying the human genome.

  • Expanded and enhanced coverage of key topics including bioinformatics, clinical trials, computation, genetics, and Bayesian methods and applications
  • Containing over 1300 articles, 182 entirely new to this edition, with more than 300 revised and updated to reflect current research and developments
  • All encompassed in 8 extensively cross-referenced volumes
The Case community has access to the Encyclopedia of Biostatistics through the Research Database list. Eventually it will also appear in the library catalog.

RIBMS: Research at the Interface of the Biological and Mathematical Sciences

A new initiative funded by the National Science Foundation will pave the way for undergraduates to get involved in the growing field of mathematical sciences becoming an indispensable part of breakthroughs in the biological sciences. Case's Research at the Interface of the Biological and Mathematical Sciences will provide opportunities for math, statistics and biology majors to collaborate across disciplinary boundaries, mentored by interdisciplinary teams of faculty. Further information is available at http://www.case.edu/artsci/ribms/ribms.html. Application deadline is November 8.

[VIA: CASE DAILY, October 30, 2006]

CALL FOR PAPERS - Advanced Mining & Use of Life Science Information

CALL FOR PAPERS - Advanced mining and use of life science information, ACS Chicago, March 2007

You are invited to submit abstracts for a session entitled "Advanced mining and use of life science information" in the division of Chemical Information (CINF), co-sponsored with the CSA Trust, at the 233rd American Chemical Society meeting in Chicago, March 25-29, 2007

We are particularly interested in papers that address the mining of large volumes and diverse sources of chemical and life science information to aid in decision making in the drug discovery process. Potential topics include (but are not limited to):

  • Development or application of data mining techniques
  • Knowledge discovery on large chemical databases such as PubChem
  • Integrating textual and structural information
  • Design of interfaces and interaction tools for complex, diverse kinds of information
  • Database querying tools and interfaces
The presentation should last about 30 minutes, including time for questions. To submit an abstract, go to http://oasys.acs.org/acs/233nm/cinf/papers/index.cgi and select the "Advanced mining and use of life science information" session. Abstracts should be submitted no later than November 17th, 2006.

If you have questions, please feel free to contact David Wild at djwild @ indiana.edu. You can find out more information about the CSA Trust at http://www.csa-trust.org/.

David Wild
Session organizer


Dr. David J. Wild, djwild @ indiana.edu
Assistant Professor

Indiana University School of Informatics

ph (812) 856-1848 - fax (812) 856-1995

1900 E. 10th St. Rm. 1128, Bloomington, IN 47406

web http://www.informatics.indiana.edu/djwild

Case in the Top 100 in Biotechnology Research

A study released Wednesday by the Milken Institute, a nonprofit, independent economic think tank in Santa Monica, Calif., places Case in the top 100 of U.S. universities in biotechnology research and turning that research into commercial applications. As for Ohio universities specifically, Ohio State University ranked the highest, at 50th, followed by University of Cincinnati, 60th; University of Akron, 65th; and Case, 68th.

[VIA: Case Daily, September 21, 2006]

Biomedical Image Award Gallery

The Biomedical Image Awards 2006 is a striking display of shapes and patterns, and illustrates the microscopic structures of living organisms in a spectacular variety of ways.

Selected by a team of expert judges from recent acquisitions by the Medical Photographic Library of the Wellcome Library, the winning images show a wide variety of subjects, most invisible to the naked eye, revealing new layers of complexity.

My favorite might be the cross-section of an old specimen of rhinoceros horn.

Upcoming Tangled Bank

Make sure to checkout the next Tangled Bank on July 19, 2006, at Salto Sobrius. Entries to be included can be submitted to host@tangledbank.net.

Informing the General Public about Nanotechnology

On October 6, 2005, the National Science Foundation (NSF) has announced a series of initiatives that will greatly expand efforts to inform the general public about nanotechnology, and to explore the implications of that fast-moving field for society as a whole.

The Nanoscale Informal Science Education Network

NSF has selected the Museum of Science, Boston, along with the Science Museum of Minnesota and the Exploratorium in San Francisco, to create and lead this network, which will also include many other science museums and research institutions (partial list below). The $20 million, five-year effort represents the largest single award NSF has given to the science-museum community, and will be a cornerstone of the foundation's multidisciplinary Nanoscale Science and Engineering Education program.

Nanotechnology in Society
NSF has selected the University of California, Santa Barbara, and Arizona State University in Tempe, Ariz., to create two new Centers for Nanotechnology in Society. These centers will support research and education on nanotechnology and social change, as well as educational and public outreach activities, and international collaborations.

In addition, building on previously supported efforts, the foundation has funded nanotechnology-in-society projects at the University of South Carolina and at Harvard University.

ChemDB at University of California, Irvine

ChemDB is a public database of small molecules available on the Web. ChemDB is built using the digital catalogs of over a hundred vendors and other public sources and is annotated with information derived from these sources as well as from computational methods, such as predicted solubility and three-dimensional structure. It supports multiple molecular formats and is periodically updated, automatically whenever possible. The current version of the database contains approximately 4.1 million commercially available compounds and 8.2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities.

Additional information:
ChemDB: a public database of small molecules and related chemoinformatics resources
Jonathan Chen, S. Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, and Pierre Baldi
Bioinformatics 2005 21(22):4133-4139

(Thank you to Gary Wiggins on the Chemical Information Sources Discussion List - CHMINF-L for pointing out this resource.)

Tangled Bank #56


Now for a Tangled Bank hosted by an Engineering Librarian...

General science, biology, and medicine are not my typical subject areas as I usually highlight resources in engineering and electronic resources available from my library. I occasionally branch off into medicine and biology as I support faculty and students conducting research in biomedical engineering.

Good science is important for everyone, and I hope this Tangled Bank promotes further discussion and thoughts, as we explore the science in spacecraft, illness, global warming, butterflies, locust, Star Wars, sex, love, and many other topics.

Outfit a spacecraft with a huge but incredibly lightweight mirror, and it can travel indefinitely, without fuel, at speeds that eventually exceed those of conventional rocket-powered craft. Joe Kissell presents Solar Sails - The next big thing in space travel posted at Interesting Thing of the Day.

Explore some of the research findings that suggest that there is an epigenetic basis to the development of lupus, an autoimmune disease that affects nearly 200 million Americans. Trevor Covert at Epigenetics News shares The Epigenetics of Systemic Lupus Erythematosus (SLE).

Jeremy Bruno at The Voltage Gate took a closer look at a recent Oprah show that discussed global warming by looking at a few inaccuracies and the shows reliance on propaganda rather than facts.

GrrlScientist presents Another Origin of Species posted at Living the Scientific Life. This essay describes an elegant Nature paper that investigates the role of homoploid hybridization in creating a new species of butterfly. (Homoploid hybridization is when the parent species and their hybrid offspring all have the same number of chromosomes).

The Different River presents WouldIntroducti

TOXNET - TOXicology Data NETwork

TOXNET (TOXicology Data NETwork) is a cluster of databases covering toxicology, hazardous chemicals, environmental health and related areas. It is managed by the Toxicology and Environmental Health Information Program (TEHIP) in the Division of Specialized Information Services (SIS) of the National Library of Medicine (NLM). TOXNET provides free access to and easy searching of the following databases:

  • HSDB (Hazardous Substances Data Bank)
  • IRIS (Integrated Risk Information System)
  • ITER (International Toxicity Estimates for Risk)
  • CCRIS (Chemical Carcinogenesis Research Information System)
  • GENE-TOX (Genetic Toxicology)
  • Tox Town
  • Household Products Database
  • Haz-Map
  • LactMed (Drugs and Lactation)
  • DART/ETIC (Development and Reproductive Toxicology/Environmental Teratology Information Center)
  • Toxics Release Inventory (TRI)
  • ChemIDplus
See the Factsheet for TOXNET: Toxicology Data Network for detailed descriptions.

Tangled Bank Host on July 5th

UPDATE: Here is the Tangled Bank I am hosting.


I will be hosting the Tangled Bank on July 5th. Submit items by email.

MOLTABLE - Chemoinformatics Portal & its Application in Bioinformatics

When a potentially useful drug is designed or discovered, it must be delivered in a way that maximizes its ability to benefit patients.

The Moltable initiatives to discover drug candidates against CANCER, AIDS, Malaria and other potentially devastating infectious diseases through chemoinformatics research. Drug candidates in various stages of research are being analyzed to discover new and promising candidates. Dynamic QSAR initiatives through 'focused' virtual library design and the results will be made 'open access' through Moltable portal (National Chemical Laboratory, Pune, India).

The portal includes links to projects, a repository for molecules, and various other resources.

Biointerphases - New Open Access Journal

The Biointerphases journal, an open access journal for the biomaterials interface community, provides an interdisciplinary platform for scientific exchange among the biology, chemistry, physics, and materials sciences communities. It offers a discussion forum for rapid dissemination of scientific theories, results, and interpretations. Biointerphases serves as a global vehicle for the biomaterials interface community as well as a platform that encourages dialog between scientists and the public with respect to cogent policy issues.

[About Biointerphases]

Biointerphases is devoted to Articles of original research, Reviews, a "Myth and Reality" section addressing controversial models and experiments, Editorial Commentary/Letters to the Editor, Perspectives on Evolving Research, Reports on Interdisciplinary Research Programs and Opinionated Essays.

Biointerphases will include all topics relevant to the study and understanding of interfaces and confined phases in biomaterial science and biophysics, e. g. such as interface spectroscopy, in vivo mechanisms, in vitro mechanisms, interface modeling, adhesion phenomena, protein-surface interactions, cell-surface interactions, biomembranes on a chip, biosensors / biodiagnostics, bio-surface modification, the nano-bio interface, biotribology / biorheology, molecular recognition, cell patterning for function, polyelectrolyte surfaces, and ambient diagnostic methods. Biointerphases is freely available online, and will be available in an annual bound volume for a nominal fee.

National Institutes of Health: Office of Science Education

The Office of Science Education (OSE) coordinates science education activities at the National Institutes of Health (NIH) and develops and sponsors science education projects in house. These programs serve elementary, secondary, and college students and teachers and the public. Users can explore the content by subject area, grade level, or format.

Students might find the career resources quite helpful when looking for an internship or job.

See About Us for more information.

(VIA: The Scout Report, Volume 12, Number 20, May 19, 2006)

Citation Advantage of Open Access Articles

The article Citation Advantage of Open Access Articles (PLoS Biology, volume 4, issue 5, May 2006) described a study that looked at the number of citations of open access articles versus pay publications.

Articles published as an immediate OA article on the journal site have higher impact than self-archived or otherwise openly accessible OA articles. We found strong evidence that, even in a journal that is widely available in research libraries, OA articles are more immediately recognized and cited by peers than non-OA articles published in the same journal. OA is likely to benefit science by accelerating dissemination and uptake of research findings.

NIH Research

The NIH Budget and the Future of Biomedical Research
Joseph Loscalzo, M.D., Ph.D.
The New England Journal of Medicine
Volume 354, Number 16, Pages 1665-1667, April 20, 2006

The "first true budgeted reduction in NIH support since 1970" is predicted for 2007. See the full article for what this may mean for biomedical research.

Case Center for Proteomics Inaugural Symposium

The Case Center for Proteomics Symposium will be on May 24 from 1 to 5 p.m. in the Wolstein Research Building Auditorium. During the symposium, four renowned researchers in the area of proteomics and mass spectrometry will make presentations, followed by a reception in the Wolstein lobby. For more information and updates regarding the seminar go to http://casemed.case.edu/proteomics/.

(Via: Case Daily - May 05, 2006)

Sigma-Aldrich Launches Collection of Biological Pathways

On April 6, 2006, Sigma-Aldrich announced the launch of PathFinder, an innovative online resource that offers a free and comprehensive collection of interactive biological pathways.

PathFinder presents biological signaling and metabolic pathways in an interactive, graphical representation of the cell that researchers can use to explore the relationships between different pathway components. The online tool provides links to appropriate, high-quality products from Sigma-Aldrich's first-in-class range, including small molecules, antibodies, enzymes, QPCR components and siRNAis for gene knockdown. Additional support is provided through links to detailed product descriptions and technical articles. PathFinder, developed in conjunction with bioinformatics specialist Protein Lounge, will be launched initially with some 20 pathways. Once completed later this year, the application will contain over 100 signal transduction pathways.

See the full announcement for more information.

(Via: Knowledgespeak, April 10, 2006)

EECS Professor Awarded $1.2 Million for Bioinformatics Research

Jing Li, an assistant professor with the electrical engineering and computer science department, was recently awarded a National Institutes of Health R01 grant for approximately $1.2 million to be used for interdisciplinary research in bioinformatics and computational biology.

(Source: Case Daily, April, 20, 2006.)

BioMed Central Journals Have RSS Feeds

BioMed Central offers RSS feeds for each of their journals.

[What is BioMed Central?]

BioMed Central is an independent publishing house committed to providing immediate open access to peer-reviewed biomedical research. Read more here...

Track Biomedical Papers Being Discussed by Bloggers

Postgenomic collates posts from life science blogs and then does useful and interesting things with that data. For example, you can see which papers are currently being discussed by neurologists, or which web pages are being linked to by bioinformaticians. It's sort of like a hot papers meeting with the entire biomed blogging community.

A RSS feed is available to track the "Posts of the day", "Current hot stories", or "Current hot papers".

[About Postgenomic]

Postgenomic aggregates posts from life science blogs and then does useful and interesting things with that data.

For example, it allows you to get an instant picture of which web sites are being heavily linked to by researchers in the medical sciences, or which papers are being cited or reviewed most often by bioinformaticians, or which buzzwords are being used the most frequently by evolutionary biologists.

It's sort of like a hot papers meeting with the entire biomed blogging community.

Sort of.

Postgenomic's primary purpose is to act as a central repository for reviews of scientific papers and for conference reports. You can help with this by adding some very simple semantic markup to your blog posts when you write a review of a paper. In this context a "review" isn't necessarily a particularly long or critical assessment of the paper (though it could be): it's simply any information that other researchers might find useful.

(Originally shared on the Science Library Pad, March 3, 2006)

Virtual Journal for Biomedical Optics

In January of 2006, the Optical Society of America (OSA) launched the Virtual Journal for Biomedical Optics.

[About Virtual Journal for Biomedical Optics]

The Virtual Journal for Biomedical Optics (ISSN: 1931-1532) consists of selected articles recently published in OSA's peer-reviewed journals. For the virtual journal, biomedical optics is considered to include research involving the interface between light and medicine or biology. Articles are selected by the editor, Dr. Gregory W. Faris, on the basis of relevancy using OCIS codes and abstract keywords.

Each issue comprises articles published in the source journals during the previous month. Thus the February virtual journal issue features articles originally published in January. Additional content such as editorials, meeting announcements, tutorials and reviews, and articles from other publications will also be solicited and published as the virtual journal expands its scope over time.

Citations to articles in the Virtual Journal for Biomedical Optics should be made to the original source journals.

[About OSA]

Founded in 1916, the Optical Society of America (OSA) was organized to increase and diffuse the knowledge of optics, pure and applied; to promote the common interests of investigators of optical problems, of designers and of users of optical apparatus of all kinds; and to encourage cooperation among them. The purposes of the Society are scientific, technical and educational. Read more at...

MEMS Technology and Biomedical Applications - Conference

The Gordon Research Conference on "MEMS Technology and Biomedical Applications" will be held at Connecticut College, New London, CT during the week of June 25-30, 2006. There is an opportunity for researchers and their students to present their work at a poster session during the conference. More information about the conference, including links to registration can be found at http://www.grc.uri.edu/programs/2006/mems.htm.

Session topics include:

  • Novel BioMEMS Sensing
  • Chemical Specificity for BioMEMS Sensing
  • BioMaterials for BioMEMS
  • MEMS Technology as a Biomedical Device Platform
  • Biologically Inspired MEMS
  • Biofluidic Microsystems
  • Lab-on-a-Chip
  • Implantable MEMS Devices
  • Applications of BioMEMS in Human Health

Several Case speakers are listed, including:

  • Horst von Recum - "Activation of gene regulation by a drug delivery microchip"
  • Carlos Mastrangelo - Tentative Title: "Microfluidics chips for integrated DNA Assays"

Medical Information Day

Tuesday, April 11, 2006, or 4-11, is "Medical Information Day". The observance recognizes the invaluable information and vast range of services medical librarians provide for their institutions and local communities.

Case is very lucky with the availability of medical information available to us through the Cleveland Health Sciences Library consisting of the Allen Memorial Medical Library and the Health Center Library.

(Thank you to ResourceShelf, April 9, 2006, for sharing this information.)

arXiv.org e-Print Archive

Hosted by Cornell University, arXiv.org is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. As of February 27, 2006, it contained over 350,000 e-prints. The major subject categories are broken down into more specific subjects that allow the user to find papers of relevance to their research. Abstracts can be viewed in html and the full papers are available in PDF. RSS feeds are available for individual archives and categories.

More Research @ CASE

The Observer (February 17, 2006) highlighted Case's new West Quad that will consist of various research programs. The initial structure contains the Cleveland Center for Structural Biology (CCSB) and the Wright Fuel Cell Group.

PLoS (Public Library of Science)

I have highlighted a couple of the Public Library of Science (PLoS) open access titles in the past (PLoS Genetics and PLoS Computational Biology). Read the testimony of a CASE student that has been using the PLOS resources.

Bioscience Funding - Ohio is #2

The Cleveland Dealer (January 23, 2006) reported that Ohio was the No. 2 spot in the Midwest for venture capital investments in bioscience last year.

The Scientist - Now with a Blog & Podcasts

The Scientist, available to the Case community in print through the Health Center Library (HCL), now offers various improvements at The Scientist web site. Thanks to the Science Library Pad blog we have word of new podcasts and blog.

The Albert Szent-Gyorgi Papers

The Scout Report in the December 2, 2005 edition shared a summary of the Albert Szent-Gyorgi Papers.

The Albert Szent-Gyorgyi Papers
are hosted by the National Library of Medicine as part of its Profiles in Science series.

Albert Imre Szent-Gyorgyi (1893-1986), a Hungarian-born biochemist, was the first to isolate vitamin C, and his research on biological oxidation provided the basis for Krebs' citric acid cycle. His discoveries about the biochemical nature of muscular contraction revolutionized the field of muscle research. His later career was devoted to research in "submolecular" biology, applying quantum physics to biological processes. He was especially interested in cancer, and was one of the first to explore the connections between free radicals and cancer. Szent-Gyorgyi won the 1937 Nobel Prize in Physiology or Medicine for his work in biological oxidation and vitamin C, and the Lasker Award in Basic Medical Research in 1954, for contributions to understanding cardiovascular disease through basic muscle research.
[About Profiles in Science]
The National Library of Medicine (NLM) is making the archival collections of leaders in biomedical research and public health available on its Profiles in Science® web site. The site, launched in September 1998, promotes the use of the Internet for research and teaching in the history of biomedical science. Many of the collections have been donated to NLM and contain published and unpublished items, including books, journal volumes, pamphlets, diaries, letters, manuscripts, photographs, audiotapes, video clips, and other materials.

Biological Informatics

Thanks to the Engineering Resources blog for sharing information about the Biological Informatics Blog.

BiologicalInformatics.info is a Subject Tracer™ Information Blog developed and created by the Virtual Private Library™. It is designed to bring together the latest resources and sources on an ongoing basis from the Internet for biological informatics (health informatics, neuroinformatics, biodiversity informatics and biomolecular informatics).

The Virtual Private Library™ is powered by Subject Tracer Bots™ that continuously search, monitor and update for custom virtual library subject(s) that are listed as an unique ontology subject tree and directory including resource utilization of blogs, wikis, listserv® and news aggregators.

Advances in Nanotechnology - Links Updated

The Scout Report (Volume 11, Number 44, November 4, 2005) has put together a collection of various nanotechnology web sites.

Interactive Concepts in Biochemistry

The Scout Report (June 24, 2005, Volume 4, Number 13) showcased Interactive Concepts in Biochemistry.

While Interactive Concepts in Biochemistry is a companion website to Dr. Rodney Boyer's Concepts in Biochemistry (2nd edition), which CASE does not own, it is still a nice multimedia web site for instruction in biochemistry.

In addition to sections that correspond to each of the book's chapters, the web site offers many opportunities for learning. It offers Concept Reviews with quizzes for elementary kinetics, logarithms, pH & buffers, Redox reactions, and thermodynamics. The web site contains various interactive animations, such as cell structure, cloning, glycolysis, or photosynthesis. Using Chemscape Chime plug-in, the web site offers interactive structure tutorials in various topics, such as DNA or kinesin. The web site also includes articles on "cutting edge" topics and various web links for further exploration.

Science and Photography Through the Microscope

From The Scout Report (Volume 11, Number 44, November 4, 2005) comes an announcement about a web site focused on microscopic images. Science and Photography Through the Microscope (a web site devoted to microscopy science education) contains images by award-winning photomicrographer Dennis Kunkel.

The Image Library contains over 1500 micrographs of scientific, biological and medical subjects photographed with light and electron microscopes. The Image Use Policy is well posted, including how educators may gain permission to use an image.

New Open Access Journal: EURASIP Journal on Signal Processing and Bioinformatics

UPDATE: Name has already changed to "EURASIP Journal on Bioinformatics and Systems Biology".

Hindawi Publishing Corporation is preparing to published a new open access journal called EURASIP Journal on Signal Processing and Bioinformatics.

[Aims & Scope]

The overall aim of EURASIP JSPB is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide area of applications into the core new disciplines of genomics, proteomics, and systems biology. The journal is intended to offer a common platform for scientists from several areas including signal processing, bioinformatics, statistics, biology and medicine, who are interested in the development of algorithmic, mathematical, statistical, modeling, simulation, data mining, and computational techniques, as demanded by various applications in genomics, proteomics, system biology, and more general in health and medicine.

Supreme Court to Look at What can be Patented

The Supreme Court will hear the case of Laboratory Corp. of America (LabCorp) v. Metabolite Laboratories. The specific patent being questioned is US 4,940,658 (July 10, 1990), titled Assay for sulfhydryl amino acids and methods for detecting and distinguishing cobalamin and folic acid deficency.

Method for determining levels of sulfhydryl amino acids, particularly total homocysteine levels in samples of body tissue from warm-blooded animals, methods of detecting cobalamin and folic acid deficiency using an assay for total homocysteine levels, and methods for distinguishing cobalamin from folic acid deficiency using an assay for total homocysteine levels in conjunction with an assay for methylmalonic acid.

Depending on how the Supreme Court resolves this case, it may have substantial implications for the patentability of business methods and even of software. See this blog for more information and a legal perspective of what could happen.

New Biological Science Awareness Tool - Faculty of 1000

BioMed Central now publishes a new web site called Faculty of 1000. Faculty of 1000 is the next generation literature awareness tool. It is a revolutionary new online research service that will comprehensively and systematically highlight and review the most interesting papers published in the biological sciences, based on the recommendations of a faculty of well over 1000 selected leading researchers.

Articles are categorized in subject areas, including biochemistry, bioinformatics, biotechnology, cell biology, chemical biology, developmental biology, ecology, evolutionary biology, genomics & genetics, immunology, microbiology, molecular biology, molecular medicine, neuroscience, physiology, plant biology, and structural biology. In addition, users can browse the "Top 10", "All Time Top 10", "Most Viewed", or the "Hidden Jewels."

[About Faculty of 1000]
Faculty of 1000 will be run by scientists for scientists, and will provide a rapidly updated consensus map of the important papers and trends across biology.

Faculty of 1000:

  • Provides scientists with a continuously updated insider's guide to the most important papers within any given field of research
  • Highlights papers on the basis of their scientific merit rather than the journal in which they appear
  • Offers the researcher a consensus of recommendations from well over 1000 leading scientists
  • Systematically organizes and evaluates the mass of information within scientific literature
  • Offers an immediate rating of individual papers by the authors' peers, and an important complement to the indirect assessment provided by the journal impact factor.

Journal of International Medical Research - Open Access Journal Title

Thanks to George S. Porter on the CHMINF-L listserv for sharing this announcement on this new open access journal. Journal of International Medical Research provides articles free on the Internet, because it operates under a page sponsorship fee system.

[About Journal of International Medical Research]

Founded in 1972, The Journal of International Medical Research has established itself as a leading journal for rapid publication of original medical, pre-clinical and clinical research.

Clinical and pre-clinical studies are welcomed as are reviews, case reports, preliminary communications and studies on new indications or new formulations of established products. Post-marketing surveillance, pharmacoeconomic and managed care studies are also invited.

Journal supplements for symposium proceedings, summaries of presentations or collections of medical, pre-clinical or clinical data on a specific topic are published and enquiries from potential sponsors of these are welcome.

All medical areas will be considered for publication including animal pharmacology, clinical pharmacology, pharmacokinetics, drug metabolism, toxicology, teratology and clinical trials.

Immunome Research - New Open Access Title

Thanks to George S. Porter on the CHMINF-L listserv for sharing this announcement on this new open access journal. BioMed Central has started publication of its newest open access journal title, Immunome Research.

[About Immunome Research]

Immunome Research is an Open Access, peer-reviewed, online journal integrating traditional laboratory research with the latest technologies, including genomics, bioinformatics and mathematical modelling.

Immunome Research is a journal of the International Immunomics Society (IIMMS). The journal aims to provide a focal point for the field of Immunomics, which lies at the intersection between traditional laboratory research and the latest research technologies. It thereby includes the sub-speciality immunoinformatics, as well as the application of large-scale genomics to the immune system. Rapidly expanding areas of particular interest include the predicting of MHC-peptide binding, mathematical modelling of viral/host interactions, and the use of gene expression arrays to model immune system pathways.

To date there has been no specialty journal covering this new and rapidly expanding domain. Researchers published their immunomics research either in general immunology journals or in bioinformatics journals. These journals generally do not have ready access to expert reviewers with knowledge in both domains - i.e. traditional immunology and bioinformatics/modelling. Furthermore, researchers interested in reading more in the area cannot easily access or find relevant articles, which are sprinkled across many different journals. The International Immunomics Society (IIMMS) has a rapidly growing membership that has expressed the need to have a high quality specialist journal to provide consistent standards to the field and provide a focal point for growth of this area.

Origin of BLAST and the Explosion of Bioinformatics

The Scientist (v.19:16, p.21, August 29, 2005) has an article about the history of BLAST and how the code allows scientists to compare a gene sequence against GenBank. Some of the off-the-chart numbers include GenBank had over 40 million sequences at the end of 2004, and that the National Center for Biotechnology Information commits 158 two-processor computers to gene sequence queries.

Environmental Health & Safety Research on Nanoparticles

As reported in the August 31, 2005, Knowledgespeak Newsletter, the Center for Biological and Environmental Nanotechnology (CBEN) of Rice University and the International Council on Nanotechnology (ICON) have released a free online database covering scientific findings related to the risks and benefits of nanotechnology. The environmental health and safety (EHS) resource, the first of its kind in the world, aims to combine vast amounts of scientific content on the effects of nanoparticles.

[CBEN Vision]
This Center aims to shape nanoscience into a discipline with the relevance, triumphs, and vitality of a modern day polymer science. Both fields have at their core a complex class of materials, are highly interdisciplinary enterprises, and have enormous potential for spawning technology. Unlike polymer science, however, nanoscience is in its infancy, and its maturation into a discipline to rival polymer science is unlikely to happen spontaneously. The Center for Biological and Environmental Nanotechnology fosters the development of this field through an integrated set of programs that aim to address the scientific, technological, environmental, human resource, commercialization, and societal barriers that hinder the transition from nanoscience to nanotechnology.

[ICON Mission Statement]

ICON’s mission is to assess, communicate, and reduce nanotechnology environmental and health risks while maximizing its societal benefit.

2005 Best Places To Work In Industry (Biobusiness)

The Scientist has issued an article the describes the best places to work in the biobusiness industry. The article lists the top 10 large and small companies. In addition, the article lists the top 10 factors people considered while surveyed for this article. The most important factor was the "work is personally satisfying." I am sure we all agree with that one.

See the full article for more information.

2 New Open Access Bioinformatics Journals

Libertas Academica has started publication of 2 new open access bioinformatics journals.

Cancer Informatics is a peer-reviewed, open-access research journal where those engaged in cancer research can turn for rapid communication of the latest advances in the application of bioinformatics and computational biological toward the discovery of new knowledge in oncology and cancer biology, and toward the clinical translation of that knowledge to increase the efficacy of practicing oncologists, radiologists and pathologists. See Cancer Informatics: aims and scope for more information.

Evolutionary Bioinformatics Online will began publication in the near future. Evolutionary Bioinformatics is an international, peer-reviewed journal focusing on evolutionary bioinformatics. There is growing awareness that to understand organismal form and function, through the use of molecular, genetic, genomic, and proteomic data, due consideration must be given to an organism's evolutionary context - history constrains the path an organism is obliged to take, and leaves an indelible mark on its component parts. Evolutionary Bioinformatics Online publishes papers on all aspects of computational evolutionary biology, and evolutionary bioinformatics. See Evolutionary Bioinformatics Online: aims and scope for more information.

[About Us - Libertas Academica]

Libertas Academica was launched in late 2004 when it was becoming increasingly apparent that the old, subscription-based, scholarly journal publishing model was rapidly being overtaken. Real advances in technology and its widespread availability combined with authors and librarians increasing frustrations at the established journal publishing business meant that significant changes were about to take place.

Libertas seeks to combine the very best of conventional journal publishing with the newest technology and freshest thinking in the area of OpenAccess journals. We also wish to expand the OpenAccess model to include text books.

New Open Access Journal - PLoS Genetics

PLoS, the Public Library of Science, announced the launch of their fourth Open Access journal on July 24th. PLoS Genetics publishes human studies, as well as research on model organisms—from mice and flies, to plants and bacteria. Topics include (but are not limited to) gene discovery and function, population genetics, genome projects, comparative and functional genomics, medical genetics, cancer biology, evolution, gene expression, complex traits, chromosome biology, and epigenetics. More information about PLoS Computational Biology can be found at the web site.

Additional titles include:
PLoS Genetics
Fulltext v1+ (2005+)

PLoS Computational Biology
Fulltext v1+ (2005+)

PLoS Biology
Fulltext v1+ (2003+)

PLoS Medicine
Fulltext v1+ (2003+)

New Open Access Journal - PLoS Computational Biology

PLoS, the Public Library of Science, announced the launch of their third Open Access journal on June 24th. PLoS Computational Biology features works of exceptional significance that further our understanding of living systems at all scales through the application of computational methods. Readers include life and computational scientists, who can take the important findings presented here to the next level of discovery. More information about PLoS Computational Biology can be found at the web site.

Additional titles include:
PLoS Computational Biology
Fulltext v1+ (2005+)

PLoS Biology
Fulltext v1+ (2003+)

PLoS Medicine
Fulltext v1+ (2003+)

Author-Driven Access to ACS Published Articles

The American Chemical Society (ACS) has several partial open access initiatives. First, ACS will submit articles to PubMed Central that were funded by National Institutes of Health (NIH) funds. Second, authors can provide links to their articles. During the first 12 months, 50 free e-prints will be available through the author's web links. After 12 months, the restriction will be listed.

For more detailed information, see Frequently Asked Questions Regarding ACS Author-driven Initiatives.

Continue reading "Author-Driven Access to ACS Published Articles"

XML and Chemical Information

Managing Information News (July 18, 2005) provided a summary of an article titled Communication and re-use of chemical information in bioscience. The original article by Peter Murray-Rust, John Mitchell, and Henry Rzepa is available freely online through the open-access journal, BMC Bioinformatics.

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. Valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture as proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.

BioEd Online

From The Scout Report, July 1, 2005, Volume 11, Number 26:
BioEd Online

Ever since the early days of the Internet, various educational organizations and foundations have sought to use the Web to disseminate important pedagogical tools to fellow educators and interested parties. This very fine site sponsored by the Baylor College of Medicine and Texas A&M University does exactly that for the field of biology with great aplomb. First-time visitors will want to start by perusing the homepage, which includes links to "Hot Topics" in biology (such as flu prevention), a "Biology News" section (which digests important news from the field), and a selection of recent additions to the site. Educators will also want to take a look through the slide sets offered here, in the PowerPoint format, which include topics such as human body systems, ecosystems, and Mendelian genetics. Additionally, the site also features a number of streaming video presentations for classroom use on a wide range of biological topics.

PubMed offers RSS

Library Stuff by Steven M. Cohen shared some great screen shots and instructions for converting a PubMed search into a RSS feed.

PubMed was designed to provide access to citations from biomedical literature.

Information Bridge - Department of Energy

The Information Bridge provides free access to full-text and bibliographic records of the Department of Energy research and development reports in physics, chemistry, materials, biology, environmental sciences, energy technologies, engineering, computer and information science, renewable energy, and other topics.

[From Information Bridge web site]
The Information Bridge consists of full-text documents produced and made available by the Department of Energy National Laboratories and grantees from 1995 forward. Additional legacy documents are also included as they become available in electronic format.

The eSkeletons Project

"The eSkeletons Project website is devoted to the study of human and primate comparative anatomy. It offers a unique set of digitized versions of skeletons in 2-D and 3-D in full color, animations, and much supplemental information. The user can navigate through the various regions of the skeleton and view all orientations of each element along with muscle and joint information. eSkeletons enables you to view the bones of both human and non-human primates ranging from the gorilla to the tiny mouse lemur. All of the large apes are represented as well as other species from different parts of the world. Many of these primates are rare or endangered species." [Description eSkeletons Project]

(First viewed on ResourceShelf)

Paleo Art Digitized

The Smithsonian National Museum of Natural History has provided online access to a selection of historical art in paleobiology.

Classic Textbooks in Science

Catherine Lavallée-Welch (EngLib) shared information about the digitization of out of print classic science texts.

Classic Textbooks in Science
, a project of the National Academy of Sciences, currently includes Heredity and Development, 2nd Edition, by John A. Moore.

Atlas of the Human Journey - The Genographic Project

National Geographic and IBM have partnered together to collect DNA samples in order to create maps of man's migratory history. The result of The Genographic Project will be to create a research database of genetic samples and the related anthropological data.

The Atlas of the Human Journey allows a user to explore photos, facts, and other information about various eras of human development and travel.

Food Safety & Applied Nutrition Spell Checker

The Center for Food Safety and Applied Nutrition (CFSAN) of the U.S. Food and Drug Administration (FDA) has developed the CFSAN Technical Lexicon. It is a downloadable spelling dictionary that can be incorporated into a user's Microsoft Office dictionaries or other software applications.

The Lexicon contains approximately fifteen thousand technical and scientific terms commonly used in the Center for Food Safety and Applied Nutrition in correspondence and regulatory documents. Names of chemicals, pathogenic species, toxic substances, and food additives are examples of the type of vocabulary included.