A very nice collaborative initiative from Ghent University !! CONGRATS !!
30 december 2009
28 december 2009
25 december 2009
Python shared
To a good friend Bruno:
Sharing with Python
Gaute T. Einevoll *
Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
A commentary on
Python for large-scale electrophysiology
by Martin Spacek, Tim Blanche and Nicholas Swindale
Researchers changing scientific fields are often surprised to discover how different the cultures in their new and old fields are. While the neuroscience culture is vibrant and stimulating in many ways, neuroscience is not a field with the strongest tradition for sharing or division of labor. In physics there has effectively been a division of labor between experimentalists and modelers for about 100 years. It was realized that it is simply too difficult for a single person or a single research group to master all techniques necessary to do the best science. Ever since, experimentalists and modelers have happily shared credit and Nobel prizes for discoveries that have only been made possible by their joint collaborative efforts. The World Wide Web was invented at CERN in Switzerland to allow for efficient sharing of the large amounts of data generated by this international particle-physics research facility.
A traditional neuroscience laboratory has been a more self-contained entity. Data has been recorded and analyzed within the group, typically with tools bought from a commercial vendor or made as side projects by the group members themselves, all under the guidance and control of a single laboratory leader. Similar to how we may imagine the operation of a 19th century physics laboratory.
But things are slowly changing also in our community. Public databases of neurobiological data have been established, the most famous probably being the Allen Brain Atlas1 set up by the philanthropist of Microsoft wealth. The Organisation for Economic Co-operation and Development (OECD) even concluded that neuroinformatics is so important that it established the International Neuroinformatics Coordinating Facility (INCF)2 in 2005 in order to promote a coordinated global development of this new field, and the open-access Frontiers Journal Series with an aim to facilitate better scientific communication between researchers was recently established with neuroscience as the pioneering field. Further, due to persistent efforts by enthusiastic individuals, neuroscientists have for 20 years or so already enjoyed free access to neural simulators such as NEURON3 and Genesis4, tailor-made for biophysically detailed neuron modeling. Lately, simulators such as NEST5, optimized for simulations of large neuronal networks, have been added to the pool of free public resources. The use of these simulators is now an integral part of the curriculum at several research schools, further contributing to the fostering of a more cohesive research community, particularly within computational neuroscience.
Free software packages tailored for experimental neuroscientists have been scarcer, and the three new packages described in the paper by Spacek et al. (2009) are thus most welcome. The packages, all developed to suit needs in the authors’ laboratory, are used for (i) generation of visual stimuli for in vivo recordings, (ii) visualization of extracellular potentials recorded by silicon multielectrodes and spike-sorting based on such data, and (iii) analysis of the extracted spike trains.
All software packages were made using the Python programming language6, and the paper of Spacek and collaborators was part of a recent special-topic issue on “Python in neuroscience” in Frontiers in Neuroinformatics. Python appears to be the new programming language of choice in many communities both inside and outside science. For outsiders the shift towards a new programming language, Python in this case, may sometimes appear to be faddish and have elements akin to a religious revival. However, Python appears to have qualities that likely will lead to a further strengthening of its position in the years to come.
For one it is “open source,” so unlike for products from commercial competitors like MATLAB, one doesn’t have to worry about licensing costs. Like the operating system Linux, or scientific knowledge for that matter, Python is largely developed by dedicated individuals who are standing on each other’s shoulders. Already a large number of Python packages have been made available, and Spacek and his collaborators say that they in fact were introduced to Python via one of its many packages. But such sharing is not unique to Python. What makes Python stand out from the crowd is that it has a clear and simple syntax which, according to the authors, “fits your brain.” The first author even states in the paper that for his part “the switch to Python has made programming a much more enjoyable and productive experience, and has resulted in greatly improved programming skills.”
The requirements for the three packages developed by Spacek and collaborators differed greatly. The visual stimulus package required, for example, real-time control over the display monitor and communication via a digital output board, controlled by specific drivers, between the stimulus and acquisition computers. The package visualizing extracellular waveforms required construction of a comprehensive graphical user interface, while the spike-train analysis package required access to efficient numerical routines established by the scientific computation community. The authors nevertheless found Python to be well suited for all three.
In the final paragraph of their paper, Spacek and collaborators trumpet: “We encourage others in neuroscience to consider Python for their programming needs(…). Rallying around a common open-source language may help foster efforts to increase sharing of data and code, efforts deemed necessary to push forward progress in systems neuroscience.” It is likely that more of us will unite behind this rallying cry as we all, experimentalists and modelers alike, realize that a closer collaboration is needed to move our science forward. We will have more fun as well.
Maybe a scientist switching to neuroscience from another field in, say, 10 or 20 years will be pleasantly surprised to discover how vigorously and efficiently we collaborate?
Footnotes
^http://www.brain-map.org/
^http://www.incf.org/
^http://neuron.duke.edu/
^http://genesis-sim.org/
^http://www.nest-initiative.org/
^http://www.python.org
References
Spacek, M., Blance, T., and Swindale, N. (2009). Python for large-scale electrophysiology. Front. Neuroinf. 2, 9. doi: 10.3389/neuro.11.009.2008.
CrossRef Full Text
19 december 2009
A bridge over troubled water
Philosopher and theologian Martin Buber reminds us that “All real living is meeting.”18 december 2009
17 december 2009
Basic Instinct
Whoever wants to pass the exam for technician in neurophysiology should know what is in this book. Basic knowledge and good study material that every lab should have available fot his technicians and people in training.
Written by a noted leader in electroneurodiagnostic technology, this book will be a standard text and reference for technologists, neurology residents, and clinical neurophysiology fellows. The first part covers the technical aspects of electroneurodiagnosis, including basic electronics and recording techniques; the second part covers the clinical applications and diagnostic utilities of electroneurodiagnosis for various central nervous system disorders. The text focuses on digital recording and includes analyses based on digital data. Emphasis is on pattern recognition, artifacts recognition, technical pitfalls, and the clinical correlates of electroencephalography. The book includes material to assist students in recognizing specific artifacts. Coverage includes principles of digital recording, electronics and electrical safety. This book will be a valuable aid in preparing for the ABRET (American Board of Registration of Electroencephalographic and Evoked Potential Technologists) certification or the neurophysiology boards. A companion Website will include a question bank and a streaming video showing how to place electrodes.
15 december 2009
Chaos games
learn about Chaos and non linear dynamics, Complex adaptive systems and deterministic Chaos by ... playing.
A nice set of java games to be found here:
14 december 2009
13 december 2009
Risus Sardonicus
From SciAm:
A toxin that forces a condemned victim to smile really seems to exist. The Greek bard Homer coined the term "sardonic grin" after ceremonial killings that supposedly took place in Sardinia, where Phoenician colonists gave to elderly people who could no longer take care of themselves and to criminals an intoxicating potion that put a smile on their face. (They were then dropped from a high rock or beaten to death.) Scientists at the University of Eastern Piedmont in Italy and their colleagues think they now have identified the herb responsible: hemlock water dropwort (Oenanthe crocata), which is common on Sardinia, where it is popularly known as "water celery." Their analysis revealed the presence of highly toxic chemicals in the plant that could make facial muscles contract into a grimace, or rictus. The finding appears in the May 22
How Couchy crazy does it get ?
Please take a seat......on this Dutch couch molded after the spectral presentation of Your EEG !!
Designers are known to have crossed the edge before..crazy ? maybe but hello .. did they not get Your attention ?
hmm.............are they thinking of a bed ?
12 december 2009
New Qeeg Handbook
The study of Quantitative EEGs and Neurofeedback offer a window into brain physiology and function via computer and statistical analyses, suggesting innovative approaches to the improvement of attention, anxiety, mood and behavior. Resources for understanding what QEEG and Neurofeedback is, how they are used, and to what disorders and patients they can be applied are scarce, and this volume serves as an ideal tool for clinical researchers and practicing clinicians, providing a broad overview of the most interesting topics relating to the techniques. The revised coverage of advancements, new applications (e.g. Aspberger's, music therapy, LORETA, etc.), and combinations of prior approaches make the second edition a necessary companion to the first. The top scholars in the field have been enlisted and contributions will offer both the breadth needed for an introductory scholar and the depth desired by a clinical professional.
*Detailed new protocols for treatment of anxiety, depression, ADHD, and PTSD
*Newest protocol in Z-score training enables clinicians to extend their practices
*LORETA diagnostic tool lets the clinician watch for changes deep in the brain through working with surface EEG patterns
From Seroto9 2 Seroto10
George Koob, director of the division of Psychopharmacology, Scripps Research Institute, La Jolla, Ca:
"The book has great merit in that the neurobiology of serotonin is quite extensive and has significant implications for our understanding of psychiatric disease and treatment. An update is sorely needed if it synthesizes the area by topic. The scope is comprehensive; I cannot think of anything missed. The utility would be as a reference source for research, and teaching at all levels from graduate school to medical school. Editors are outstanding scientists in the field. Choice of authors is equally outstanding. ... There is really nothing out there that pulls the world's literature on serotonin together. It is hard to get a real solid perspective on how serotonin does everything from impulsivity in suicide to depression to anxiety to mediate the effects of LSD and a tome that explains all of this would fill a niche. Readers would be graduate students, researchers, medical students, residents and university teachers."
Robert Carey, VA Medical Center, Upstate Medical University, Syracuse, NY, CA:
"There has been a major shift away from Dopamine to Serotonin so this is a very timely book proposal and the selected editors/authors are excellent choices to put together an important and successful book."
Boris Quednow, Psychiatric Hospital, University Zurich, Switzerland:
"I waited long for such a handbook of serotonin. This book was overdue for a long time and I think that it has the chance to be a bestseller in this area. The scope is indeed wide but appropriate and the utility of this book is - without any doubt - very high. The editors are highly experienced researchers in this field and the proposed authors belong to the leading scientists in serotonin research. "
11 december 2009
A network view on Psychiatry
10 december 2009
A view from the top
How to encourage big ideas
December 9, 2009 by Peter Dizikes Enlarge
Graphic: Christine Daniloff
(PhysOrg.com) -- A new study suggests certain types of funding -- which provide more freedom and focus less on near-term results -- lead to more innovative and influential research.
Scientists are much more likely to produce innovative research when using long-term grants that allow them exceptional freedom in the lab, according to a new study co-written by MIT economists.
The work shows that biologists whose funding encourages them to take risks and tolerates initial research failures wind up producing about twice as many highly influential papers as some peers whose funding is dependent upon meeting closely defined, short-term research targets.
“If you want people to branch out in new directions, then it’s important to provide for their long-term horizons, to give them time to experiment and potentially fail,” says Pierre Azoulay, an associate professor at the MIT Sloan School of Management, and an author of the study. “The researcher has to believe that short-term failure will not be punished.”
The results are contained in a working paper released this fall, “Incentives and Creativity: Evidence from the Academic Life Sciences,” by Azoulay, Gustavo Manso, an assistant professor at Sloan, and Joshua Graff Zivin, an associate professor of economics at the University of California, San Diego.
06 december 2009
05 december 2009
04 december 2009
PTSD: Phantasmagorically Truly supercalidotiously dumb
Truly, the woo doth flow. Like a river. Like the energy from a supernova. From Bozeman, Montana, where, apparently they don’t have enough woo and have to import it from Texas. I haven’t seen such a massive pseudoscientific abuse of physics and chemistry in quite a long time.
EEG back to Basics
Why consult encyclopedic references when you only need the essentials? Practical Approach to Electroencephalography, by Mark H. Libenson, MD, equips you with just the right amount of guidance you need for obtaining optimal EEG results! It presents a thorough but readable guide to EEGs, explaining what to do, what not to do, what to look for, and how to interpret the results. It also goes beyond the technical aspects of performing EEGs by providing case studies of the neurologic disorders and conditions in which EEGs are used, making this an excellent learning tool. Abundant EEG examples throughout help you to recognize normal and abnormal EEGs in all situations.
03 december 2009
02 december 2009
EEG book
Reading EEGs: A Practical Approach focuses on pattern recognition and pattern comparison. The concepts of pattern recognition are developed in a logical fashion based on appearance rather than disease process. The book teaches waveform recognition so that the reader can generate a differential diagnosis based on that recognition. This book also incorporates a question-and-answer format that is effective for students at multiple levels of training. A unique feature of the book is that it follows a teaching methodology in which concepts are developed sequentially and logically.
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