Archive for the ‘General information’ Category

Call for INCF Abstract Submissions

Posted on March 14th, 2013 in Force11, General information, News & Events | No Comments »

6th INCF Congress of Neuroinformatics in Stockholm, Sweden August 27 – 29, 2013

Call for abstract submissions

Neuroinformatics 2013 is now accepting abstracts, submission this year is hosted by Frontiers in Neuroscience. When you submit your abstract, please indicate if you would like to be considered for an oral presentation by choosing “Oral presentation”.

Submit your abstract here!

We are accepting submissions until April 8th.

NIF Announcement Team

INCF.org

Call for papers: Frontiers in Neuroinformatics special topic “Recent advances and the future generation of neuroinformatics infrastructure”

Posted on March 3rd, 2013 in Force11, General information, News & Events | No Comments »

Call for papers:

*Frontiers in Neuroinformatics special topic *“Recent advances and the
future generation of neuroinformatics infrastructure”

Topic Editor(s): *Xi Cheng*, *Daniel R. Weinberger*, *Daniel Marcus*, *John
Van Horn*, *Venkata S. Mattay*, *Qian Luo*

Deadline for Abstract Submission: 31 Jul 2013

Deadline for Article Submission: 31 Oct 2013

The huge volume of multi-modal neuroimaging data across different
neuroscience communities has posed a daunting challenge to traditional
methods of data sharing, data archiving, data processing and data analysis.
Neuroinformatics plays a crucial role in creating advanced methodologies
and tools for the handling of varied and heterogeneous datasets in order to
better understand the structure and function of the brain. These tools and
methodologies not only enhance data collection, analysis, integration,
interpretation, modeling, and dissemination of data, but also promote data
sharing and collaboration. This Neuroinformatics Special Issue aims to
summarize the state-of-art of the current achievements and explores the
directions for the future generation of neuroinformatics infrastructure. We
welcome submissions from the following 4 topic areas: 1) data archiving, 2)
data processing and workflow, 3) data mining, and 4) system integration
methodologies. The data archiving section focus on novel methods for
efficient collection, storage and query of huge volume neuroimaging data,
genetics data, and all other related measures as well as meta-data and
processing results. The data processing and workflow section emphasizes
methods that facilitate large-scale parallel data processing tasks under
the heterogeneous computational environment. The data mining section
emphasizes novel data analysis methodologies to extract meaningful
information from the data. Finally the system integration section focus on
the best practices and novel approaches to integrate multiple systems
(database, workflow, ware house, etc). To be more specific, we would like
to invite a spectrum of subtopics from the 4 areas, including but not
limited to:

1.Data archiving

1.1.Novel data annotation and visualization

1.2.Archiving automation/simulation/de-identification/compression/quality
control/ontology, etc.

1.3.Novel storage architecture (e.g., grid, web storage, XML, OO, …, etc.)
and search engine

1.4.Data warehousing

2.Data processing and workflow

2.1.Novel neuroimaging data processing algorithms, packages and libraries

2.2.Distributed/parallel algorithms design (cluster/GPU/FPGA/cloud/HPC, etc)

2.3.Neuroimaging workflow design

2.3.1.Visualization/annotation

2.3.2.Workflow for distributed/collaborative environment

2.3.3.Provenance, meta data management

3.Data mining

3.1.Novel multi-modal integration methods

3.2.Feature extraction and visualization methods

3.3.Novel machine learning methods

3.4.Novel applications (biomarker detection/clinical
application/imaging-genomics/brain-computer-interface/publication mining,
etc.)

4.System integration methodologies, frameworks, architectures and best
practices

4.1.Integration of different software components, e.g., database/data
warehouse/workflow system/data analysis package and libraries.

4.2.Cross-platform, cross-modality integration

4.3.Cross-domain integration

4.3.1. Integration of imaging database with other types of databases

4.3.2. Integration of imaging workflow with other types of workflow

4.4.Distributed system integration

4.4.1. Data synchronization/query/transaction control/access control/single
sign on/processing

More Information:

http://www.frontiersin.org/neuroinformatics/researchtopics/recent_advances_and_the_future/1577

If you have questions regarding whether your research fits in the scope of
this scpecial issue, please send inquiries to
infrastructure.neuroinfo@gmail.com

UC now paying for Open Access!

Posted on October 30th, 2012 in Anita Bandrowski, Force11, General information, News & Events | 2 Comments »

Hot off the press, from the desk of the Chancellor we just received a note about open access publishing that I would like to celebrate and share.

Beginning this week, the University of California campuses have launched
a pilot open access fund for scholarly articles.  This fund will help
offset open access publishing charges for authors who do not have grant
funds available to cover them.  Eligible charges include Article
Processing Charges (APCs) and Open Access (OA) fees for fully open
access journals.  Funds from the pilot may not be used for color
charges, page charges, illustration charges, or submission charges.
Articles must be made freely available at the time of initial
publication, without any embargo periods.”

Essentially, UCSD is now offering its’ scientists cash, the magic word, to help to publish in open access journals. This will hopefully solve the biggest quandary that many scientists have with open access publishing, it is expensive. Will this mean that UC is moving toward publishing only open access articles as some have suggested?

Top 25 Accessed Databases at NIF from Sept. 4 – Oct. 4, 2012

Posted on October 5th, 2012 in General information, Inside NIF, News & Events | No Comments »

Here are the top 25 Accessed Databases at NIF from Sept. 4 – Oct. 4, 2012.

1.  Grants.gov/Opportunity
2.  AntibodyRegistry/ABs
3.  BioNOT/Negation
4.  ABCD/Brain Regions
5.  AllenInstitute/MouseBrainAtlas
6.  AmiGO/Genes
7.  NIF Integrated Nervous System/Connectivity
8.  BAMS/Brain Regions
9.  NIF Registry/info
10. NIF Registry/Info
11. OneMind/BioBanks
12. BrainMaps/Atlas
13. ClinicalTrials/ClinTr
14. NIF Integrated Software/Info
15. NIF Integrated Animals/Available
16. NIF Annotation/Info
17. Drug Related Gene Database/DRG
18. AddGene/Plasmids
19. bioDBcore/Databases
20. RePORTER/CurrentNIHGrants
21. WikiPathways/ChemPathway
22. BioGRID/Interactions
23. BrainInfo/Brain Region
24. Gemma/Microarray
25. OMIM/Genes

Top 25 Search Terms at NIF from Sept. 4 – Oct. 4, 2012

Posted on October 5th, 2012 in General information, Inside NIF, News & Events, Uncategorized | No Comments »

Here are the top 25 Search Terms at NIF from Sept. 4 – Oct. 4, 2012.

1.  antibodyregistry
2.  database
3.  “DOMMINO – Database Of MacroMolecular INteractiOns”
4.  “Rhode Island Biobank”
5.  “Frontal Lobe”
6.  “Purkinje Cell”
7.  “Satellite Cell”
8.  hippocampus
9.  “Diencephalon”
10.  “Drug Related Gene Database”
11.  cerebellum
12.  “ALSA – The Australian Longitudinal Study of Ageing”
13.  “Amygdala”
14.  “Angular Gyrus”
15.  “Brainstem”
16.  “Cerebellum”
17.  “Forebrain”
18.  “Hypothalamus”
19.  “Mitral Cell”
20.  “Astrocyte”
21.  “Cingulate Cortex”
22.  “Cone Cell”
23.  “Hippocampus”
24.  “Medium Spiny Neuron”
25.  “Anterior Nucleus of the hypthalamus”

Frontiers in Addiction Research Mini-convention – Oct 12, 2012, New Orleans, LA

Posted on September 21st, 2012 in General information, Inside NIF, News & Events | No Comments »

Frontiers in Addiction Research Mini-convention
Sponsored by the National Institute on Drug Abuse

Friday, October 12, 2012

Sheraton New Orleans Hotel, 500 Canal Street, New Orleans, LA

Seating is limited.  Additional information and registration can be found at: https://seiservices.com/nida/frontiers2012/

The NIDA mini-convention, Frontiers in Addiction Research, held in conjunction with the annual Society for Neuroscience Meeting, will feature outstanding scientists who will present their cutting-edge research on the neurobiology of drug abuse and addiction.  The NIDA mini-convention features four symposia, the SfN Jacob P. Waletzky Memorial Lecture and a poster session for early career investigators.  The agenda this year includes:

8:00 am- 8:15 am                  Welcome: NIDA Director

8:15 am- 9:35 am                   Ghrelin, Leptin and Insulin Modulates Reward

9:35 am-10:10 am                 Jacob P. Waletzky Memorial Lecture

10:35 am-12:15 pm                 Role of Phagocytes in Synaptic Plasticity & Remodeling in the Nervous System

12:15 pm- 2:15 pm                  Early Career Investigators Poster Session

2:15 pm- 3:35 pm                  Brain Energetics and Neurotransmission: Fueling Neurons and Glia

3:50 pm-5:25 pm                   Central Nervous System Immune Signaling and Addiction

NIDA will also hold several other events at the Society for Neuroscience meeting, including:

1)      Toni S. Shippenberg Memorial Symposium – Friday, October 12, 2012, 6:00-7:30 p.m.

2)      Julius Axelrod Lecture and Poster Session – Sunday, October 14, 2012, 6:30-9:00 p.m.

3)      NIDA/INSERM Workshop on US-France Collaboration on Drug Abuse and Addiction Research – Monday, October, 15, 2012, 6:30-9:00 p.m.

4)      NIH Grant Workshop for Early Career Investigators – Tuesday, October 16, 2012, 6:30-9:00 p.m.

Information on these events can also be found at:  https://seiservices.com/nida/frontiers2012/

NIF Webinar – Tuesday, August 21, 2012 at 11:00 am PDT (2:00 pm Eastern DT)

Posted on August 10th, 2012 in General information, News & Events, Webinar Announcement | No Comments »

Hello everyone.

Please mark your calendars.

The next NIF Webinar will be held on  Tuesday, August 21, 2012 at 11:00 am PDT.   Please join Dr. Anita Bandrowski as she discusses NIF 4.5.

The following is a description of the Webinar:

What genes are regulated by drugs of abuse? Find what you are looking for at NIF. The Neuroscience Information Framework (NIF) provides easy access to the largest collection of neuroscience information on the web. Whether you need data, tools, papers, materials, services, webinars, blogs or funding opportunities, NIF’s semantic search can help. See how NIF can enhance your research by visiting http://neuinfo.org.

NIF has just released a brand new interface to make it easier to search and browse our contents (over 150 databases). Join us for a tour of the new NIF on 21st of August, at 11 am PDT (2 pm EDT) on the web.

This resource is supported by the NIH and is freely available to researchers and the public.

Date and Time: Tuesday, August 21, 2012 • 11:00-12:00 PDT
Topic: NIF 4.5
Presenters: Dr. Anita Bandrowski
URL: http://connect.neuinfo.org/webinar

Mark your calendars! See you there.

The Neuroscience Information Framework (NIF) hosts a semi-regular Tuesday Webinar series on topics focused on collaborating with NIF, getting involved in building the NIF vocabulary, using NIF portal resources, as well as other appropriate NIF topics.

--
NIF Communications Team
UC San Diego
3rd Floor, Atkinson Hall
9500 Gilman Drive, MC 0446
La Jolla, California 92093

858-822-0755
http://www.neuinfo.org

NIF Webinar – Tuesday, August 7, 2012 at 11:00 am PDT

Posted on July 31st, 2012 in General information, News & Events, Webinar Announcement | No Comments »

Hello everyone.

Please mark your calendars.

The next NIF Webinar will be held on  Tuesday, August 7, 2012 at 11:00 am PDT.   Please join Tom Hawkins as he discusses Zebrafishbrain.org: developing a community neuroanatomical resource.

The following is a description of the Webinar:

We are in the process of developing zebrafishbrain.org. Our objective is to create a web-based repository containing and communicating the most up to date information about the zebrafish brain. In this webinar, I will introduce our approach to developing this resource, including detail about sources and types of data, how we present these data, image annotation, and ontology. The resource is at an early stage of development: we are still working on the structure and have not begun data population in earnest. We have a considerable amount of in-house data ready to input, and we are also planning to solicit contributions from the wider zebrafish neuroscience and comparative anatomy community. Our ideas about how best to achieve this will be presented. Once the resource structure is complete and the volume of data has grown, then we are keen to forge links with similar resources in other species. To ensure easy interoperability in the future, we are currently using the ZFIN ontology in the creation of this resource, but the integration of the ZFIN ontology with other ontologies needs to be addressed. Given the expertise of the NIF group, we hope to initiate a discussion on the best way(s) to achieve this.

Date and Time: Tuesday, August 7, 2012 • 11:00-12:00 PDT
Topic: Zebrafishbrain.org: developing a community neuroanatomical resource
Presenters: Tom Hawkins
URL: http://connect.neuinfo.org/webinar

Mark your calendars! See you there.

The Neuroscience Information Framework (NIF) hosts a semi-regular Tuesday Webinar series on topics focused on collaborating with NIF, getting involved in building the NIF vocabulary, using NIF portal resources, as well as other appropriate NIF topics.

--
NIF Communications Team
UC San Diego
3rd Floor, Atkinson Hall
9500 Gilman Drive, MC 0446
La Jolla, California 92093

858-822-0755
http://www.neuinfo.org

Top 25 Search Terms at NIF from June 11 to July 11

Posted on July 12th, 2012 in General information, Inside NIF, News & Events | No Comments »

Here are the top 25 search terms at NIF from June 11 to July 11:

1.            antibodyregistry

2.            database

3.            “Cingulate Cortex”

4.            “Purkinje Cell”

5.            “Hypothalamus”

6.            “Commissure of Fornix”

7.            cerebellum

8.            “Brainstem”

9.            “Forebrain”

10.          “Drug Related Gene Database”

11.          “Cerebellum”

12.          “Frontal Lobe”

13.          schizophrenia

14.          “Hair Cell”

15.          “Mitral Cell”

16.          “Oligodendrocyte Precursor Cell”

17.          glioma

18.          hippocampus

19.          receptive field

20.          “Amygdala”

21.          “Cerebral Crus”

22.          “Cone Cell”

23.          “Fornix”

24.          antibodyregistry gene:grm1

25.          “Anterior Nuclear Group”

Top 25 Accessed Databases at NIF – June 11 to July 11

Posted on July 12th, 2012 in General information, Inside NIF, News & Events | No Comments »

Here are the top 25 Access Databases at NIF from June 11 to July 11:

1.            Grants.gov/Opportunity

2.            GENSAT/GENSAT

3.            CCDB/All Information

4.            AntibodyRegistry/ABs

5.            SumsDB/Activation Foci

6.            ResearchCrossroads/Grants

7.            NIF Integrated Nervous System/Connectivity

8.            BrainInfo/Brain Region

9.            Drug Related Gene Database/DRG

10.          RePORTER/CurrentNIHGrants

11.          ClinicalTrials/ClinTr

12.          ModelDB/Models

13.          BioNOT/Negation

14.          BAMSCN/Con

15.          NIF Integrated Animals/Available

16.          DrugBank/Drugs

17.          OMIM/Genes

18.          BrainMaps/Atlas

19.          NeuroMorpho/NeuronInfo

20.          GEO/Gene Expression Omnibus

21.          NIF Integrated Software/Info

22.          AllenInstitute/MouseBrainAtlas

23.          Gemma/Microarray

24.          HumanBrainAtlas/Michigan

25.          Neurofed/GovernmentPeople