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Community News
- 10-13 March 2013
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We are honored to announce, "Neuroplasticity and Cognitive Modifiability," an International conference on Brain and Cognitive Intervention. More information (in English, Geramn, French, and Spanish) is available on the site: www.brainconference.com
- April 23, 2012
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The deadline to submit abstracts for Neuroinformatics 2012 has been extended to May 1st due to overwhelming demand. Click here for the submission page.
Review results will still be sent out mid-May and the early-bird registration deadline is still June 1st.
For more information about the event>
- April 17, 2012
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This year the Klinikum rechts der Isar conference center in Munich will host both Neuroinformatics 2012 on September 10-12 and the Bernstein Conference 2012 immediately after, on September 12-14.
Keynote speakers of Neurinformatics 2012 include Gordon Shepherd from Yale Medical School, Atsushi Miyawaki from RIKEN BSI in Wako, Japan, Michael Brecht from the Bernstein Center for Computational Neuroscience in Berlin, Germany, Sonja Grün from Forschungszentrum Jülich in Jeulich, Germany, and Russell Poldrack from the University of Texas at Austin.
As in previous INCF Neuroinformatics Congresses, INCF will be accepting abstract submissions for those who wish to display posters or give a live computer demonstration. You can view more information about abstract submissions and the poster and demos here. The deadline for abstract submissions is April 20, 2012.
Confirmed speakers for the Bernstein Conference 2012 include Kwabena Boahen from Stanford University, Moritz Helmstaedter from MPI Munich, Maryann Martone from UCSD, and many others.
The Bernstein Conference 2012 is, too, accepting abstract submissions for poster presentations. Additionally, accepted abstracts will be published in Frontiers in Computational Neuroscience. The deadline for submissions is May 11, 2012. There is more information here.
Attendees can register for both Neuroinformatics 2012 and the Bernstein Conference 2012 at a reduced rate from either site.
For more information about the Neuroinformatics 2012 and the Bernstein Conference 2012>
- March 20, 2012
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This four-day course will cover a basic introduction to ontology design principles and usage, specifically ontology considerations dealing with anatomy, including the application of anatomy ontologies in the context of evolutionary phenotype comparison. There will be hands-on exercises that will develop ontology skills and provide exposure to different software applications that deal with the various areas of evolutionary biology.
This event will be held at the National Evolutionary Synthesis Center in Durham, NC. Tuition will be about $250, and participants are responsible for their own travel costs, including transportation and accommodation, though a limited number of travel scholarships from NESCent and the Phenotype Ontology RCN are available for US-based participants.
You can apply here. The deadline for applications is Friday, April 6, 2012. Keep in mind that your application is not a guaranteed spot in the workshop. If there are any questions about the application process, please contact academy@nescent.org.
For more information about the event>
- March 16, 2012
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Do you have a task in biomedical or clinical informatics that will benefit from the use of ontologies or ontology-based technology? Want to brainstorm application design and development questions? Want help incorporating the NCBO Web services into your application?
Join the National Center for Biomedical Ontology in their first ever NCBO Hackathon at Stanford University in Stanford, California! This two-day event will include intensive hands-on sessions to assist in the development of your applications using NCBO Web services, with presentations covering a spectrum of topics from application design to coding.
Registration is $25. Spots are limited, however, so register immediately.
For more information and to register for the event>
- March 15, 2012
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Although there have been recent efforts to build ontology to assist in the representation, retrieval, and assessment of adverse event reports, questions still remain as to how the ontology might be used in conjunction with the new and existing information models. Are ontology terms to be added to records as keywords to retrieval? Or should information models be revised in favor of a more ontological analysis?
Participants must have experience that can shed new information on these questions, or are actively developing adverse event reporting systems and can serve to evaluate feasibility and utility of workshop proposals.
Topics of interest include, but are not limited to:
-Existing information models, their strengths, weaknesses, and competency criteria.
-Ongoing efforts to build new information models for adverse event reporting or analysis.
-Case studies demonstrating information systems that integrate ontology in clinical systems.
-Reports of new developments in adverse event ontology.All submissions are due by April 30th, 2012.
To read the full details>
- March 8, 2012
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Eric Courchesne, PhD, of the University of California, San Diego has been studying autism since the mid-1980s when he first encountered a young teenage boy stricken with the disease. Since then, Courchesne has been dedicated to his research and has been studying the anatomical brains of autistic individuals in hopes of finding the origin of the disease and, thusly, a possible course of treatment.
Courchesne studied the brains of individuals of various ages, from toddlers to adults, in order to find something that set autistic brains apart. Eventually, he noticed a pattern in development: up until the age of 5, autistic children possessed a much larger prefrontal cortex, up to 67 percent more neurons than average. This research suggests that at birth, autistic children have an abundance of neurons in an average-sized brain that, over the course of the next few years of development, sprout thousands of branches to other neurons, and in turn those neurons send out another vast number of connections to other neurons. This overwiring may interfere with the normal development of language and social behavior in young children and account for the excess brain size seen in the MRI scans Courchesne had taken in his early research.
Using MRI scans in conjuction with blood and behavioral tests, "it might be possible to identify infants at risk at a much younger age, when circuits are just being established," Courchesne says. And once the children are identified, they could be treated to help their brains develop properly.
To read the full news>
- March 6, 2012
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Researchers and surgeons at the Moores Cancer Center at the University of California, San Diego are conducting trials for a breakthrough treatment for glioblastoma, a deadly form of brain tumor. This treatment involves the direct injection of Toca 511, a viral vector designed to kill brain cancer cells while leaving healthy cells unharmed by delivering a cytosine deaminase (CD) gene selectively to the cancerous cells.
As of now, the current treatment option for glioma is rather ineffective, as despite the surgical removal of as much of the tumor as possible followed by radiation and chemotherapy, the tumor usually recurs. Moreover, the tumors are located in a delicate arena and, as Clark Chen, MD, PhD, director of stereotactic and radiosurgery at UC San Diego's Moores Cancer Center, explained, this viral treatment "may provide a way to destroy the cancer cells without disrupting delicate neurocircuitry."
For information about participating in this clinical trial, visit www.tocagen.com/clinicaltrials or www.clinicaltrials.gov and search for "Toca 511."
To read the full news>
- Feb 24, 2012
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Recent findings from an ongoing study about the effects of HIV and antiretroviral therapy on the central nervous system reveal that larger waistlines are indeed linked to decreased mental functioning, or neurocognitive impairment (NCI), and moreso than to general obesity.
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In an experiment conducted by J. Allen McCutchan, MD, of the University of California at San Diego and his team, their analyses revealed several key factors associated with NCI: older age, a longer time living with HIV, diabetes, and an increased waistline. Their study also concluded that people suffering from NCI averaged waistlines four inches bigger than those without the impairment. Furthermore, there was no correlation between NCI and an increase in body mass index (BMI) as there is with general obesity.
To read the full news>
- Oct 6, 2011
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In this challenge, a full stack of EM slices will be used to train machine learning algorithms for the purpose of automatic segmentation of neural structures.
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Anybody can participate in the challenge. The only requirement consists of filling up the registration form here to get a user name and password to download the data and upload the results.
The best ranked methods will be presented a the workshop previous to the IEEE International Symposium on Biomedical Imaging (ISBI) 2012
Please Visit the website for full details about the challenge>
- Oct 4, 2011
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President Barack Obama will soon honor University of California, San Diego Bioengineering Professor Shu Chien in a White House ceremony for the seven eminent researchers to receive the National Medal of Science, the highest honor bestowed by the United States government on scientists and engineers. Chien is the only engineer among the seven medalists announced last week.
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Shu Chien, a professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering, is a world leader in the study of how blood flow and pressure affect blood vessels. Chien’s research has led to the development of better diagnostic tests and treatments for atherosclerosis, which refers to the hardening of the arteries, and other diseases.
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To read the full news>
- Oct 3, 2011
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Biologists at the University of California, San Diego have identified more than 70 genes that play a role in regenerating nerves after injury, providing biomedical researchers with a valuable set of genetic leads for use in developing therapies to repair spinal cord injuries and other common kinds of nerve damage such as stroke.
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While scientists in recent decades have gained a good understanding of how nerve cells, or neurons, develop their connections in the developing embryo, much less is known about how adult animals and humans repair or fail to repair those connections when axons are damaged.
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To read the full news>
- Oct 3, 2011
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Technology Conference and Society will be held at University of California, Los Angeles, USA from 16-18 January. This Conference will address a range of critically important themes in the various fields that address the complex and subtle relationships between technology, knowledge and society. Plenary speakers include some of the leading thinkers in these areas, as well as numerous paper, colloquium and workshop presentations.
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A written paper can be submitted to The International Journal of Technology, Knowledge and Society, a fully refereed academic Journal. Virtual participants may also submit papers for consideration by the Journal. All Conference participants who have finalized their registration will receive a complimentary online subscription to the Journal. This subscription is valid until one year after the Conference end date.
- Sep 26, 2011
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The San Diego Supercomputer Center at the University of California, San Diego, has launched what it claims is thelargest academic-based cloud storage system in the country. The system is capable of an initial raw 5.5 petabyte of storage and is 100 percent disk-based with high-speed 10 gigabit Ethernet network interconnections.
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SDSC's Cloud uses two Arista Networks 7,508 switches, providing 768 total 10 gigabit Ethernet ports for more than 10Tbit/s of non-blocking, IP-based connectivity. Users can store their data in the cloud for as low as $3.25 per Month for 100GB or $32.50 per Terabyte per Month with no transfer costs.
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To read the full article>
- Sep 26, 2011
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The Texas Advanced Computing Center (TACC) at the University of Texas at Austin announced on September 22nd, 2011 that it will deploy and support a world-class supercomputer with comprehensive computing and visualization capabilities for the national open science community. Made possible by a $27.5 million grant from the National Science Foundation (NSF), this new deployment is part of the NSF "eXtreme Digital" (XD) program, an integrating system for the majority of NSF's high end computational resources made widely available to U.S. researchers.
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The new system, "Stampede," will be built by TACC in partnership with Dell and Intel to support the nation's scientists in addressing the most complex scientific and engineering problems. Stampede is anticipated to go into full production in January 2013 and will be available to researchers for four years.
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To read the full press release>
- Sep 20, 2011
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The Journal of Librarianship and Scholarly Communication (ISSN 2162-3309), a quarterly, peer-reviewed, open-access publication for original articles, reviews and case studies that analyze or describe the strategies, partnerships and impact of library-led digital projects, online publishing and scholarly communication initiatives, is looking for papers to go on its inaugural issue.
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The editors are seeking papers that expertly discuss and represent these core dimensions of scholarly communication: author rights advocacy, repository management, traditional and non-traditional publishing models, citation metrics, copyright management, digital collection development, and the impact of any of the above on the system of scholarly exchange and reward (e.g. tenure and promotion).
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For more information, visit the submission page>
- May 24, 2011
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NIH will be holding Advanced Medical Imaging Developments and Applications for Neuroscience Research on June 9th, 2011 in Bethesda, MD. It is a great opportunity to join NIH staff, neurobiologists and medical imaging scientists for a free symposium to explore and discuss:
* Current medical imaging technologies
* Applications of medical imaging in brain disease and disorders
* Research collaboration opportunities between neurobiologists and medical imaging scientists and ways to facilitate such efforts. - Please register online by May 26th!
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For more information, visit the event page>
- May 18, 2011
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NIMH, The National Institute of Mental Health has an update on science education resource. The Brain Basics, an animated video describing how the brain works, has opened to provide information on basic brain processes and strcuture, related mental disorders and illnesses, and ongoing researches on these disorders. The information are presented in animated videos on different levels of brain activity, including how the brain develops, how genes and the environment affect the brain, the basic structure of the brain, how different parts of the brain communicate and work with each other, and how changes in the brain can lead to mental disorders, such as depression.
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To Brain Basics link>
- May 17, 2011
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UCSD neuroanatomist Jacopo Annese has undertaken an unprecedented effort to create highly detailed digital images of the brains of 1,000 deceased men and women. Each of the donated brains will be sliced into 2,500 to 2,700 hair-thin slices, digitally scanned, then turned into three-dimensional anatomical maps that can be accessed by researchers around the world via by computer. The Digital Brain Library, as the project is known, is meant “to provide novel different ways to look at and consider the brain,” Annese said. “For example, a neurologist will be able to examine and compare the brain of a subject or patient using different modalities, such as MRIs and corresponding microscopic images. He will be able to look at very large landscapes of the brain, in 2-D and 3-D, or zero in on individual cells or structures. He can investigate whether hypotheses about a neurological condition in life are validated by post-mortem physical evidence.
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To read the full article>
13th International Congress of Stereology
- May 10, 2011
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13th International Congress of Stereology (ICS-13) which will be held at Tsinghua University, Beijing, P. R. China, from October 19 - 23, 2011. It is the 13th quadrennial conference of the International Society for Stereology (ISS). The ICS-13 will include oral and poster sessions, prospective authors will be invited to present their latest results in all areas of stereology. It is a pleasure to request you to consider submitting your latest research to ICS-13. The deadline for submitting your abstracts is May 20, 2011.
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For more information about the conference, visit the congress website
First Articles In New Neuroscience Journal - Brain Connectivity - Debut Online
- April 26, 2011
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The The new neuroscience journal,Brain Connectivity, set to become the premier source of cutting-edge basic and clinical research contributing to a better understanding of how structural and functional connections in the brain are organized, develop, and are altered in neurological disorders, launches with the publication of four compelling articles. The full issue will be released in early May. Brain Connectivity, a bimonthly peer-reviewed journal, is published by Mary Ann Liebert, Inc.
To ensure that scientific findings are rapidly disseminated, each article will be published Instant Online within 72 hours of acceptance, with fully typeset, fast-track publication within 4 weeks. - To read the full announcement on the debut of Brain Connectivity, please visit here >>
- Allen Institute For Brain Science Announces First Comprehensive Gene Map Of The Human Brain
- April 13, 2011
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The Allen Institute for Brain Science has released the world's first anatomically and genomically comprehensive human brain map, a previously unthinkable feat made possible through leading-edge technology and more than four years of rigorous studies and documentation. The unprecedented mappings are the foundation for the Allen Human Brain Atlas, an online public resource developed to advance the Institute's goal to accelerate understanding of how the human brain works and fuel new discovery among the global research community.
- To read the full announcement on the Human Brain Atlas, please visit here >>
- Brain juice and stem cells: Revisiting an ancient view of cerebrospinal fluid
- March 21, 2011
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In the second century, the Greek physician Galen viewed the brain itself as a mere holder of cerebrospinal fluid.. The neuroanatomical term “thalamus,” referring to part of the brain stem, comes from the Greek word for “chamber,” implying that the brain was mainly important as a holder for CSF. The philosopher Descartes thought that the brain was a pump that moved the fluid around to do the brain’s work. Swedish scientist Emanuel Swedenborgreferred to the CSF as a “spirituous lymph” and a “highly gifted juice.” Alas, recent history has not been so kind to CSF. Its reputation as a dynamic, life-giving part of the nervous system receded. Instead, it came to be regarded as a supporting player, providing a fluid cushion for the brain and maintaining its ionic balance. An article from Boston's Children's Hospital shows new take on this issue and how acients might have not been completely wrong.
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To read the article >>
- March 18, 2011
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7th Stem Cell Research & Therapeutics Conference will be taking place on May 26-27, 2011 in Boston, MA. This forum provides cutting-edge information on developments in all areas of stem cell research including the biology, medicine, applications, regulations, and the business of Stem Cells. Join in the discussion with colleagues in academia and industry to share and learn about the latest research technologies and novel discoveries in the area of stem cells. Gain insight into the issues and challenges facing the research community and hear success stories from industry leaders. Register by March 26th for 20% discount.
For more information about the conference, visit their website >>
- March 9, 2011
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JoVE, the Journal of Visualized Experiments, has published its 1000th article. Since its inception in 2006, JoVE has forever changed the way the world's brightest scientific minds can share information. A picture is worth a thousand words, and a video infinitely more. This concept put JoVE at the forefront of a new and vital way of disseminating scientific techniques and methodologies in order to accelerate scientific progress and increase productivity of research, particularly in the biological and medical sciences. In JoVE's landmark 1000th article, the group of Professor Laura Niklason of Yale University's Department of Biomedical Engineering demonstrates tissue-engineering of fully functional lungs in a bioreactor.
To read the full press release website >> - To watch actual 1000th article by JoVE website >>
SEPUBLICA is an Extended Semantic Web Conference workshop. The mission of the SEPUBLICA workshop is to bring together researchers and practitioners dealing with different aspects of semantic technologies in the publishing industry. How is the SW impacting the publishing industry? How is our experience of publications changing because of SW technologies being applied to the publishing industry? The workshop also includes the ELSEVIER BEST SEMANTIC PAPER AWARD (submission deadline: Feb 28, 2011) and Springer LNCS post-proceedings.
For more information visit SEPUBLICA website >>The Second Annual Brain Development Conference will be held in Vancouver, Canada from June 19th to June 21st. The conference will explore innovative research into brain development, and what these findings mean for patients, families, clinicians, researchers, and policy makers. NeuroDevNet is the first Canada-wide initiative to study children’s brain development from both basic and clinical perspectives. The conference will also bring together researchers with passion and expertise in brain development and neurodevelopmental disorders with a focus on autism spectrum disorders, cerebral palsy and fetal alcohol spectrum disorders. Also, experts in brain imaging, the interaction of genetics and the environment, and modeling will discuss their findings and the meaning of these results for children and families.
For more information on Brain Development Conference, please visit the website >>The ISBS, International "Stress and Behavior" society invites you to two conferences. 15th International "Stress and Behavior" Neuroscience and Biopsychiatry Conference will be held in St. Petersburg, Russia from May 16th to May 20th, 2011. 16th International"Stress and Behavior" Neuroscience and Biopsychiatry North American Conference will be held in New Orleans, USA from June 22nd to June 25th, 2011. This is an annual nternational event gathering scientists and psychiatrists from around the world to share an interest in stress-evoked brain disorders in both humans and animals.
For more information regarding the ISBS's conference, please visit their website >>- February 7, 2011
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Semantic Web Journal is looking for papers to be published on its special issue regarding new models of scientific publishing. Fields of interests are Computer Supported Collaborative Work, Linked Data, eScience and Workflow-driven tools, and Digital Libraries. The goal of this special issue is to develop web-based science publication system with rapid, seamless and automatic integration, availability of information across different disciplines, and reproducibility of the research reported and truly data-driven science.
Read the full information about the special issue by Semantic >>
On December 7th, 2010, Macmillan Publishers Ltd. announced the launch of Digital Science (http://www.digital-science.com/), a new division of the company and a new kind of scientific information enterprise. Digital Science will focus on providing software tools and information to researchers and research administrators in their everyday work, with the ultimate aim of making research more productive through the use of technology.
Read the full announcement about Digital Science by Macmillan >>The new National Resource for Network Biology - based at the University of California, San Diego School of Medicine - will work to grant researchers access to more and better tools for conducting advanced studies of biological systems. By applying torrents of data from the operations of biological networks to the development of new treatments and therapies, the NRNB will strive to result in sophisticated models of how human systems function in the next five years.
Read the full news release from the UC San Diego Health System »Images, a new resource developed and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at the National Institutes of Health, already provides more than 2.5 million images and figures from medical and life sciences journals. The database will enable users to search for images based on keywords and a variety of other parameters.
Read the full article from NIH News »This solicitation addresses the challenges of creating a set of exemplar national and global data research infrastructure organizations (dubbed DataNet Partners) that provide unique opportunities to communities of researchers to advance science and/or engineering research and learning.
Read the full solicitation from the NSF Office of Cyberinfrastructure (OCI) »Scientists from the Montreal Neurological Institute and Hospital – The Neuro, McGill University have discovered our brains' ability to determine the shape of an object without any visual or tactile information. With specially-coded sounds, it was shown that we can convey shape information as long as the spatial relation is coded in a systematic way. This discovery opens new possibilities for aiding those who are blind or with impaired vision.
Read the full article from the Montreal Neurological Institute and Hospital »Researchers from the University of Minnesota, Washington University, Mass General Hospital, Harvard, and UCLA will work together on an endeavor to discover how the human brain is wired. In hopes to understand the complexity of the connectome, researchers will be using MRI, new technology platforms, and the Connectome Scanner, to see detail no one has seen before.
Read the full article from the Singularity Hub »Geron Corp., a local company in Menlo Park, California, took charge of running the world's first clinical trial for stem cell therapy. Although only 10 people enrolled in the clinical trial, it was a success for the United States - beating other countries to the trial stage. While the world watches, so will Californian voters as they see where their $3 billion is invested.
Read the full article from the SFGate »Over a span of five years, NIH plans to invest $60 million to help junior investigators find positions at US universities post-graduation and receiving a research degree. Ten awards will be awarded in the Fall of 2011. The deadline to apply is January 21, 2011.
Read the full article at GenomeWeb Daily News» [Paid Subsciption Required]Read the overview of awards and find out how to apply»
Ever since its launch in December 2008, the JCB DataViewer has increased in its popularity and usage. About 15,000 users access the JCB DataViewer each month. With improvements on download formats, upload process, image viewing, and overall layout, the JCB DataViewer strives to improve the user experience of the sharing of image data from published articles.
Read the full article from the Journal of Cell Biology (JCB)»Galaxy is an internet based program that provides a trackable, reproducible method for genomic data analysis, and aims to eliminate problems in research that stem from differently analyzed data. The team involved in developing the Galaxy resource believes that an open, web-based approach to genomic analysis will remove the variability stemming from the use of different, unsourced programs.
Read Galaxy Project paper published in Genome Biology»Visit the Galaxy Project website»
From Riken Research - Databases are becoming increasingly important in the life sciences as a key tool for deriving results. The Bioinformatics And Systems Engineering Division (BASE) is drawing worldwide attention for its SciNeS information infrastructure for handling the vast amounts of data generated through routine research in the life sciences. “A database is not merely a container for data, it is also a place where even life can evolve,” says Tetsuro Toyoda, the director of the BASE. “We can create useful biological resources from information resources by selecting useful genes from databases, designing new genomes, and returning them to the world of living organisms. What databases are needed to realize rational organism design? That is the question we attempt to answer.” To inspire creative use of databases for genome design, the BASE is holding its first International Rational Genome Design Contest.
Read the contest announcement at Riken Research Frontlines»A collaborative effort betwen the NIH, the FDA, and several non-profit groups has resulted in the mapping of a large collection of Alzheimer's Disease biomarkers, the largest expansion of information on the disease in recent history. The study collected information from 800 different brains at different stages of the disease, ranging from the as-of-yet-unaffected to the severely incapacitated, and has resulted in more than100 new drug studies aiming to slow or stop the progression of the disease entirely.
The project, called the Alzheimer's Disease Neuroimaging Initiative (ADNI), has spurred similar collaboration in the field of Parkinson's research, with a 40 million dollar collaborative research initiative by the Michael J. Fox Institute beginning in the next year. Particiants of the ADNI study attribute the success of their study to the heretofore unseen freedom of information that was the standard for the Alzheimer's study.
Read the full article at the New York Times»
A group of Researchers at the Polytechnic University of Madrid, Spain, have developed a tool to automatically compile bioinformatics resources cited in newly published papers, creating the first automatically curated, searchable bioinformatics database. Although the automatically curated Bioinformatics Resource Inventory (BIRI) only contains 230 resources, it is still in its prototype stage. The algorithm used for automating BIRI can extract resources and their functionality with 94% and 88% accuracy, respectively. Although the total number of resources is smaller than in comparable databases, BIRI is the only one of its kind that is automatically curated.
Read the full article at GenomeWeb Daily News» [Paid Subsciption Required]
Read the paper published in BMC Bioinformatics»
Over the next four years the National Human Genome Research Institute plans to move into the next phase of its electronic medical records research program. NHGRI plans to give out around $25.5 million in grants to fund investigators involved starting a coordinating center for research support. the Electronic Medical Records and Genomics network (eMERGE) that was founded in 2007 will continue to play an important part in the combining of electronic medical recods with DNA biorepositories for use in large-scale, high-throughput genomics research projects.
Read more at the Vanderbildt University homepage for the eMERGE project.
From the Gonzo Labs website - The dreaded question. “So, what’s your Ph.D. research about?” You take a deep breath and launch into the explanation. People’s eyes begin to glaze over… At times like these, don’t you wish you could just turn to the nearest computer and show people an online video of your Ph.D. thesis interpreted in dance form? Now you can. And while you’re at it, you can win $1000, achieve immortal geek fame on the Internet, and be recognized by Science for your effort.
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