Archive for the ‘General information’ Category

Olympus competition

Posted on September 2nd, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

Olympus would like to invite you to submit several of your images and/or digital video clips to the 2014 Olympus BioScapes Digital Imaging Competition, which will honor extraordinary microscope images of life science subjects. Up to five images or videos can be entered via the Internet. Entries for the contest can be uploaded through a web browser directly to the Olympus servers at the following URL:

http://www.olympusbioscapes.com/enter.asp

The deadline for new entries is September 30, 2014.

The winners of the competition are tentatively scheduled to be published in Scientific American.

A note about the contest: First prize will be Olympus microscope or Camera equipment valued at $5,000. Nine additional winners will also receive valuable prizes from Olympus. Each person entering can submit up to five movies, images, or image sequences. It is not necessary for people entering the competition to be users of Olympus equipment. Winners will be notified in late October, and publicly announced in December, 2014.

Comment requested: Academic credit for reviewing

Posted on August 22nd, 2014 in General information, News & Events | No Comments »

This seems a very interesting blog written by Rebecca Lawrence. The link is below.
I am re-posting it for the NIF community.


Link to original blog: http://blog.f1000research.com/2014/08/22/peer-review-service-recognition-orcid-casrai-recommendations-need-your-feedback/


Laura Paglione (Technical Director, ORCID) and I (Rebecca Lawrence) have been co-chairing the CASRAI Peer Review Services Working Group to look at the best way to recognise referee reports as a formal output in for example an ORCID profile. This project has looked at the peer review of a wide range of outputs from articles (open, closed, pre- and post-publication peer review), to grants, conference abstracts, and the review ofuniversities/faculties/departments.


We have now reviewed options for linking peer review service activities with a person identifier such as ORCID, and developed recommendations for data fields, descriptors, persistence, resolution and citation. We now need your feedback!  We are inviting interested subject experts from all these areas to review and comment on the draft outputs of this working group; the deadline for comments is Friday, September 12th 2014. In order to participate, please follow the instructions below.


1) Access the “Document Details” page here, which will provide information about the document as well as a link to download the file.
2) On the “Document Details” page click the link in the “Name” row to download the document.
3) Once you have reviewed the document, return to the “Document Details” page. Click on “add a comment” on the upper left hand side of the “Document Details” table to open the comment form.
4) Please complete one comment form for each term about which you wish to provide feedback. Commenting follows the steps below:
a) In the “Subject” line, reference the term number to which you are referring in your comment. (Example: D04)
b) Complete the comment box with your first comment.
c) Please ignore the items “Section” and “Item” as you have already addressed these by providing the term number in the Subject line.
d) If you would like to expand upon your comment by providing a proposed solution, please do so in the “Proposed Solution” field. This field is optional.
e) For security reasons, please slide the lock button at the bottom of the form to the right.
f) If you have no other comments to add click “Save” at the bottom of the form. Please note that we strongly prefer for each comment to address only one term at a time.
g) If you are commenting on multiple terms click “Save and add another” at the bottom of the form. Please note that you will not be required to re-enter your contact information for each added comment.

 


We really hope you will take this opportunity to provide your feedback on these recommendations so that we can ensure that the final output successfully achieves the goals of this project: proper recognition of the huge amount of unpaid and often invisible effort researchers put in throughout their careers to the essential task of reviewing the work of others.


I have been co-chairing the CASRAI Peer Review Services Working Group together with Laura Paglione (Technical Director, ORCID) to look at the best way to recognise referee reports as a formal output in for example an ORCID profile. This project has looked at the peer review of a wide range of outputs from articles (open, closed, pre- and post-publication peer review), to grants, conference abstracts, and the review of universities/faculties/departments.


We have now reviewed options for linking peer review service activities with a person identifier such as ORCID, and developed recommendations for data fields, descriptors, persistence, resolution and citation. We now need your feedback! We are inviting interested subject experts from all these areas to review and comment on the draft outputs of this working group; the deadline for comments isFriday, September 12th 2014. In order to participate, please follow the instructions below.

  1. Access the “Document Details” page here, which will provide information about the document as well as a link to download the file.
  2. On the “Document Details” page click the link in the “Name” row to download the document.
  3. Once you have reviewed the document, return to the “Document Details” page. Click on “add a comment” on the upper left hand side of the “Document Details” table to open the comment form.
  4. Please complete one comment form for each term about which you wish to provide feedback. Commenting follows the steps below:
  • In the “Subject” line, reference the term number to which you are referring in your comment. (Example: D04)

Have a great idea for a company? Check out the Brain Start Up Challenge

Posted on August 6th, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

Overview
The National Institutes of Health (NIH) has a significant portfolio of inventions available for licensing. The Center for Advancing Innovation (CAI) has evaluated many of them to identify those with the strongest commercial viability
The Heritage Provider Network, the NIH, and CAI are launching a start-up Challenge to exploit these opportunities

 

Phases
Phase 0: Enter Challenge: Teams provide information regarding the invention they have chosen to develop their business plan around, details and backgrounds of the members of their team, and how team members meet eligibility requirements. Teams also outline their intent to participate in the Challenge

Phase 1: Elevator Speech: Teams develop a two minute elevator speech via recorded video; a 350 word executive summary outlining potential commercial product(s) and company vision. Winners of this phase will move on to Phase 2: Business Plan

Phase 2: Business Plan: Teams develop a 10-page business plan with a detailed financial plan; a 20 minute “live” pitch presented to the challenge judges. The winners of this phase will receive a $2500 award per team that is provided by CAI and The Heritage Provider Network as well as move on to Phase 3: Start-up

Phase 3: Start-up: Teams launch their start-ups, including incorporation, license negotiation, and executing other regulatory/developmental needs

For more information check out the
http://www.brainstartupchallenge.org/overview.html

Don’t like to go searching for gut viruses? Use a computer instead, they are much cleaner

Posted on July 26th, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

The Neuroscience Information Framework often gets questions about what types of things can be found in the data about brains presumably because people would rather poke in brains than data.

However, some of our bioinformatics colleagues from the other side of town (at SDSU) that really didn’t want to go searching though their gut contents did it virtually and discovered a new highly prevalent virus.

Actually this is a bacteriophage that was found in samples from about half of gut microbiomes sampled and cleanly deposited as data in various databases.

Now there is a whole new reason to look at databases that I never thought of. They are just a lot less messy!!!

See more about the phage here: http://newscenter.sdsu.edu/sdsu_newscenter/news.aspx?s=75082

Neuroinformatics 2014: abstract submission extended to April 27

Posted on April 8th, 2014 in Anita Bandrowski, Author, General information, News & Events | No Comments »

The yearly INCF Congress provides a meeting place for researchers in all fields related to neuroinformatics. This year, the congress will take place August 25-27 in Leiden, Netherlands.


Keynotes will be given by:

- Margarita Behrens, Salk Institute, La Jolla, CA, USA
“The epigenome and brain circuit changes during postnatal development”
- Dmitri (Mitya) Chklovskii, Howard Hughes Medical Institute Janelia Farms, Ashburn, USA
“Can connectomics help us understand neural computation? Insights from the fly visual system”
- Daniel Choquet University of Bordeaux, France
“A nanoscale view into the dynamic of AMPA receptor organization in synapses”
- Ila Fiete, University of Texas, USA
“Neural codes for representation and memory”
- Michael Milham, Child Mind Institute, New York, USA
“Emerging models for biomarker identification”
- Felix Schürmann, École Polytechnique Fédérale de Lausanne, Switzerland
“In silico neuroscience – an integrative approach”

LINKS

Submit your abstract here, latest April 27: http://www.neuroinformatics2014.org/abstracts

Registration is open at http://www.neuroinformatics2014.org/registration

Watch the NI2014 promo video: http://www.youtube.com/watch?v=aEudq3SOwK0

The congress poster is available for download at http://www.neuroinformatics2014.org/documents/a0_poster_nov_2013

The International Neuroinformatics Coordinating Facility (INCF) is an international organization launched in 2005, following a proposal from the Global Science Forum of the OECD to establish international coordination and collaborative informatics infrastructure for neuroscience – and currently has 17 member countries across North America, Europe, Australia and Asia. INCF establishes and operates scientific programs to develop standards for neuroscience data sharing, analysis, modeling and simulation while coordinating an informatics infrastructure designed to enable the integration of neuroscience data and knowledge worldwide and catalyze insights into brain function in health and disease.

The NIA Butler-Williams Scholars Program (formerly Summer Institute on Aging Research) is accepting applications for an intensive introduction to aging research

Posted on January 24th, 2014 in Anita Bandrowski, General information | No Comments »

This workshop for investigators new to aging research is focused on the breadth of research supported by the National Institute on Aging, including basic biology, neuroscience, behavioral and social research, geriatrics and clinical gerontology. As an offering through the Office of Special Populations, the content will include a focus on health disparities, research methodologies, and funding opportunities. The Butler-Williams Scholars Program (B-W Scholars) is one of the premier short-term training opportunities for new investigators. New researchers are defined as those who have recently received the M.D., Ph.D. or other doctoral level degree. The B-W Scholars Program affords participants with unparalleled access to NIA and NIH staff in an informal setting.

The B-W Scholars Program is sponsored by NIA with support from the National Hartford Centers of Gerontological Nursing Excellence.

The 2014 B-W Scholars Program will be held August 4-8, 2014 in Bethesda, Maryland. Support in most cases is available for travel and living expenses.

Applications are due March 28, 2014.

Researchers with an interest in health disparities research are encouraged to apply. Applicants from diverse backgrounds, including individuals from underrepresented racial and ethnic groups, individuals with disabilities and women are always encouraged to apply for NIH support. Applicants must be U.S. citizens, non-citizen nationals, or permanent residents.

Please view more information on the NIA web site: www.nia.nih.gov/about/events/2013/butler-williams-scholars-program-2014

Please feel free to circulate the above message to potential applicants.

For more information, please contact:

Ms. Andrea Griffin-Mann
Office of Special Populations
National Institute on Aging
National Institutes of Health
griffinmanna@mail.nih.gov

The 2014 Series of PACE Data Mining Boot Camps Kicks Off on February 26-27

Posted on January 4th, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

Each day, our society creates 2.5 quintillion bytes of data (that’s 2.5 followed by 18 zeros). Conventional statistical analysis and business intelligence software are not designed to capture, curate, manage and process large quantities of data generated by most enterprises.

The PACE Boot Camps provide the Big Data community with conceptual and hands-on training. Learn the critical predictive data analytics techniques and tools that contribute to accurate, actionable and agile insights. Boot Camp training includes –

• Overview: Data Mining, Machine Learning, and Statistics
• Overview of CRISP-DM: Cross Industry Standard Process for Data Mining
• Introduction to Data Mining Tools
• Preprocessing the Data
• Learning Algorithms Implementations
• Model Evaluation and Validation
• Data Mining Trends, Applications and Guidelines

The Boot Camps are held at the San Diego Supercomputer Center on the campus of UC San Diego.

REGISTER NOW FOR THE 2014 SERIES OF BOOT CAMPS @ pace.sdsc.edu/boot-camps

FOR MORE INFORMATION:
paceinfo@pace.sdsc.edu
858.534.8321
pace.sdsc.edu

Vasculature Morphogenesis: Synopsis of three related articles by Halina Witkiewicz, Phil Oh and Jan Schnitzer

Posted on January 3rd, 2014 in Data Spotlight, Essays, General information | No Comments »

The following is is a guest blog by Krystyna Gutowska.
The topic is a set of three articles by Witkiewicz et al. previously blogged about by NIF as an exemplar of open access publishing and a new open review process utilized by the Faculty of 1000 journals.

Common sense dictates that inhibiting malignant tumor growth (cancer) should be possible by inhibiting formation of new blood vessels. An artistic vision of that belief was painted in 1940 by Diego Rivera “The Hands of Dr Moore” (San Diego Museum of Art in San Diego). In 1972 Judah Folkman presented the concept for therapy of solid tumors by the anti-agiogenesis treatment [Greek angeion = vessel] for which he became well known. Yet, the quest for such treatment has not resulted in finding the cure for cancer, so far.

Screen Shot 2014-01-06 at 9.32.10 AM

In countless review articles the formation of tumor vessels was presented graphically to reflect researcher’s current understanding of how it was supposed to happen at the cellular and molecular level. Instead of such artistic and graphic representations, the three studies published in F1000Research on January 10th 2013 provide photographic documentation of the process that turned out to be different from previously imagined. Nobody had expected blood elements to be produced at the site of new tissue growth first and subsequently single cells to assemble around them into vessels. That would have been counter-intuitive; after all, to handle any fluid one needs a vessel. Besides, the blood formation after birth was supposed to be localized in bone marrow (medulla ossea), not extramedullary. Therefore the new vessels were assumed to be formed first and filled with blood next. That misconception prevailed in science for a long time. The essential contributing factor was the false belief on how the red blood elements were formed. Specifically, how the erythrocyte precursors (erythroblasts) were eliminating their nuclei to become anucleated erythrocytes, meaning: red cells without nucleus.

Paradoxically, the concept of the nucleus being separated from cytoplasm by expulsion (resembling separation of egg yolk from the white) came from 1967 morphological studies that used electron microscopy, just like the 2013 studies discussed here. Although the same methodology was used at both times, the animal models subjected to the ultrastructural analysis were different. The critical difference was the type of analyzed tissue (bone marrow or spleen versus tumor). In the bone marrow and spleen the erythrogenesis is relatively rare and to observe it the process had to be experimentally stimulated by inducing anemia in dogs or mice. However, the tumor-hosting mice used recently were not subjected to any pathogenic treatment except the surgical implantation of cultured tumor cells into dorsal skin fold of the animals. In that model the erythrogenesis was spontaneous and frequent enough for capturing images of various stages. The expulsion of the nucleus from the erythroblasts was not happening and macrophages (the cells said to internalize and digest the released nuclei) were rare in that environment. The nuclei were degraded in the process of erythrogenic autophagy not by the macrophages but by the very cells they were a part of. Each erythrogenic cell was remodeled into a few smaller red vacuoles by a nucleo-cytoplasmic conversion. No nuclear waste was released for macrophages to clean up. Such red vacuoles are no longer cells, although they have been referred to as the erythrocytes (red cells). The 2013 studies use the term erythrosome (red body) as a synonym for erythrocyte because it describes the sub-cellular nature of those blood elements better. The cells converting into erythrosomes were visually recognizable in tissue sections and their location outside bone marrow was evident.

The erythrogenesis turned out to be the central element of the vasculature formation induced locally by the growing tumor or by healing of the surgical injury inflicted by the implantation of the tumor cells; figuratively speaking and literally, i.e., as a source of energy and as a structural morphogenetic element chemotacticly attracting cells. (Erythrocytes are known to secrete high energy molecules, ATP). Those ultrastructural studies demonstrated for the first time that the extramedullar hematopoiesis and vasculogenesis were inseparable in live animals; hence, the term ‘vasculature’ included blood and vessels. Historically, the term ‘angiogenesis’ (expansion of existing vessels) was replaced by ‘neovasculogenesis’ (generation of new vessels from bone marrow derived precursor cells). Now, the most appropriate term appears to be ‘vasculature morphogenesis’ (formation of blood and vessels from local tissue stem cells).

In the first article the authors discuss the implications of the new findings for malignant as well as non-malignant tissue or organ morphogenesis (the organoblasts concept) and for tissue definition. The second article shows formation of a capsular vasomimicry that could potentially lead to spreading of tumor cells to various locations by fusing with morphologically similar lymphatic vessels or veins, i.e. to metastasis. The third article deals with tumor energy metabolism and explains the over half a century old Otto Warburg’s conjecture by cellular heterogeneity of tumors. That connection was missed by metabolic studies based on samples isolated from tissues because the isolation process destroys the tissue. Also missed was the role for the anaerobic metabolic pathway discovered by Warburg during cell division, when the structural changes in the mitochondria indicate their temporary functional disability. That reversible malfunction correlates with a particular stage of the cell cycle (mitosis).

The 1967 conclusion on the mechanism of the erythrocytic enucleation by expulsion of the nucleus derived form pathologically changed systems was erroneously extrapolated to systems not modified experimentally. Consequently it had a long-lasting and misleading effect on multiple studies in vascular biology. The appealing concept of inhibiting angiogenesis to stop tumor growth suffered from lack of understanding the cellular interactions leading to the vasculature formation (blood as well as vessels). To study those interactions the tissue must be preserved. Electron microscopy supported by immunocytochemistry (using antibodies to identify specific molecules in situ) is the method of choice for such purpose. The observations reported in the three articles discussed here appear of profound significance for tissue morphogenesis in general, not only in malignancy.

Refocusing on inhibiting tumor vasculature formation, with the full force of currently available technologies, presents a realistic chance to cure solid tumors in large number of patients despite the tumors’ genetic diversity perpetually introduced during cell divisions. Such strategy would not interfere with proliferation of normal cells that does not result in tissue growth. One prominent example is renewal of the gut epithelium. From clinical point of view the gut epithelium is critically important because of the role it plays in absorption of nutrients.

2 computational neuroscience postdoc positions open at GMU

Posted on September 6th, 2013 in General information | No Comments »

Postdoctoral Research Fellows

George Mason University, Krasnow Institute for Advanced Study in Fairfax, Va. (USA), invites applications for several Postdoctoral Research Fellow positions available immediately in the Center for Neural Informatics, Neural Structures, and Neural Plasticity (krasnow.gmu.edu/cn3) headed by Prof. Giorgio Ascoli.

The successful applicants will join a collaborative multidisciplinary team at the cutting edge of the development and dissemination of digital tools and resources for neuroscience. The Ascoli Lab is funded by the National Institutes of Health, the National Science Foundation, the Office of Naval Research, the Air Force Office of Scientific Research, the Intelligence Advanced Research Projects Activity, and Keck. These jobs are particularly suited for computationally minded researchers seeking exposure to the burgeoning field of neuroinformatics.

(1) One or more candidates will join the NeuroMorpho.Org project-a free, public, centralized repository of neuronal digital reconstructions. Originally designed to facilitate the lab’s own research, NeuroMorpho.Org has firmly established itself as a powerful resource for the neuroscience community, with millions of downloads and data usage in over 200 publications by other labs since its 2006 public release. The position(s) are particularly suited for computer-savvy neuroscientists with knowledge and interest in axonal and dendritic morphology. These positions will also entail modeling and simulation of neuronal structure, quasiautomated neuronal reconstruction systems, handling of large experimental data sets, and collaborative use of time-lapse confocal microscopy with subcellular genetic reporters.

(2) One or more applicants will join the Hippocampome.Org project-a knowledge base of the hippocampal circuitry at the mesoscopic-level of neuronal types. The goal of Hippocampome.Org is to enable real-scale, biologically realistic neural network simulations of hippocampal connectivity, dynamics and function. Expected contributions of the successful candidate(s) include design and implementation of optimal protocols for identifying and extracting experimental information from published literature and continuous development of the associated Web portal. The postdoc(s) will also develop or adapt analytical approaches to quantify the spatial distributions of somatic, axonal, and dendritic densities; as well as software to support team efforts in data management, integration and accessibility. Experience or interest in GPU computing and outstanding motivation to publish will be put to good use.

Requirements:  We seek candidates with a strong quantitative background and an advanced degree (Ph.D. or master’s) in neuroscience, bioinformatics, computer science, electrical or software engineering, bioengineering, computational biology, mathematics, physics, or other related fields. Candidates should exhibit enthusiasm and independence; as well as the ability to work in a fast-moving interdisciplinary team including faculty, other postdoctoral and predoctoral trainees, technicians, and undergraduate research assistants. Candidates are expected to demonstrate excellent attention to details, organizational skills, and exemplary verbal and written communication skills. Knowledge in one or more areas of neuroanatomy, neurophysiology, axonal and dendritic morphology, or hippocampal structure and activity are desired.

Review of applications will begin on October 4, 2013, and continue until the positions are filled. For full consideration, applicants must apply for position number F9755z at http://jobs.gmu.edu/; and complete and submit the online application. You will be required to upload the following documents: (1) a full CV including a list of publications as a single upload; (2) copies of two representative scientific publications as a single upload; (3) a one-page research interest description highlighting any previous experience with programming languages (C/C++, Java, HTML, Ruby, R, Python, Perl, NEURON, Matlab, php, etc.), different operating systems, development and maintenance of relational databases, and Web applications; and (4) a list of the names, e-mail addresses, and phone numbers of three references.

BioCreative User Interactive Task – Request

Posted on September 4th, 2013 in General information, Jonathan Cachat, Maryann Martone, News & Events | No Comments »

The Neuroscience Information Framework is proud to support the BioCreative effort (http://www.biocreative.org) whose goal is bridging the gap between text mining and biocuration.

One activity BioCreative is currently recruiting for is a User Interactive Task (IAT) where a domain expert for a biocuration task is recruited to test a system.

This study is conducted remotely and is time flexible, as long as the evaluation is performed by September 25.  There are two levels of participation: full (involves actual curation of a selected corpus (about 60 abstracts total), completing a user survey, and being listed as co-author on the BioCreative IAT overview article) and partial (involves performing basic pre-defined tasks at the system’s website, completing a user survey and being acknowledge in the BioCreative IAT overview article).

BioCreative has 9 systems and one of them is EGAS (http://bioinformatics.ua.pt/software/egas/), a web-based platform for biomedical text mining and collaborative curation, supporting manual and automatic annotation of concepts and relations. In this case related to protein interactions in biomedical corpus related to neurological diseases.

Since NIF’s community expertise is on neurosciences BioCreative wanted to ask for our help to recruit suitable participants. Specially, they are in need for a couple of participants for full testing of EGAS.

The benefits to biocurators participating in this activity are multifold, including:

  • direct communication and interaction with developers
  • exposure to new text mining tools that can be potentially adapted and integrated into the biocuration workflow
  • contribution to the development of text mining systems that meet the needs of the biocuration community
  • dissemination of findings in a peer-reviewed journal article.

Here is the website for BioCreative IAT: http://www.biocreative.org/tasks/biocreative-iv/iat-task-biocurators/

Link to EGAS system and task description: http://www.biocreative.org/media/store/files/2013/egas.pdf

To register, select EGAS as the system in the registration page:

http://www.biocreative.org/tasks/biocreative-iv/iat-task-biocurators/#registration