Create Brain Image Library.md

Brain Image Library.md

@@ -1,59 +1,105 @@
 # Brain Image Library
 ## Description
-The Brain Image Library (BIL) will support the goals of the BRAIN Initiative
-Cell Census Network (BICCN) by providing a portal to the entire set of
-images submitted by the participating BICCN labs.  High-performance
-computational resources with high-bandwidth access to this library are
-available both through BIL and the XSEDE program, and will allow analysis
-of these datasets at scale.
+The Brain Image Library (BIL) is a national public resource enabling
+researchers to deposit, analyze, mine, share and interact with large brain
+image datasets.  BIL encompasses the deposition of datasets, the integration
+of datasets into a searchable web-accessible system, the redistribution of
+datasets, and a computational enclave to allow researchers to process
+datasets in-place and share restricted and pre-release datasets.  BIL is the
+designated repository for microscopy data produced through the NIH BRAIN
+Initiative.
 
 # Roles
-[Primary Investigator] Alex Ropelewski ([email protected])
-[System Hardware/Software] Greg Hood ([email protected])
-[Website/Submission Portal] Luke Tuite ([email protected])
-[other names to be added shortly]
+Please use [email protected] for any Brain Image Library issues or
+questions in lieu of contacting people listed here directly.
 
-## Objectives
-* Construct and operate a large-scale storage platform suitable for housing
-  many thousands of image datasets totaling many petabytes in size.
+[Primary Investigator] Alex Ropelewski ([email protected])  
+[MPI – Biologic Imaging] Simon Watkins ([email protected])  
+[MPI – Molecular Biosensors and Imaging] Marcel Bruchez ([email protected])  
+[Computational Hardware/Software] Greg Hood ([email protected])  
+[Networking Support] Kathy Benninger ([email protected])  
+[Image Data] Arthur Wetzel ([email protected])  
+[Website/Submission Portal] Luke Tuite ([email protected])  
+[Microscopy/Cell Biology] Alan Watson ([email protected])
 
-* Host a metadata portal to allow searching through the metadata of
-  these datasets.
 
-* Host an image portal to allow rapid access to images from these datasets.
+## Objectives
+* Permanent repository for high-quality brain microscopy datasets
+    – Brain images of mouse, rat, human, other mammals and model organisms
+    – Targeted experiments, including connectivity between cells and
+      spatial transcriptomics ( *FISH)
+    – Historical collections
 
-## In-scope
-* Accept confocal microscopy image datasets from BICCN or other
-  Brain Initiative laboratories
+* Provide HPC computing capability local to the data for pre-submission
+data processing and post-submission exploration
+    – Enclave access to pre-release data
+    – Research access to restricted-access, secured data
 
-* Accept datasets of other types (e.g. neuron morphologies) that are derived
-  from or relate to image datasets housed at BIL
-
-* Provide Globus and FTP-based access to all public datasets
+* Provide user access and support
 
-* Provide project-only access to BICCN collaborations, allowing members
-  to share and operate on datasets prior to publication
 
+## In-scope
+* Accept original microscopy image datasets from investigators.  Provide text
+for inclusion in Resource Sharing Plans.  There is no-charge to contribute
+data to BIL or access BIL services.
+* Accept higher-level datasets of other types (e.g. neuron morphologies) that
+are derived from or relate to image datasets housed at BIL.
+* Provide data-transfer support including network analysis to find transfer
+bottlenecks, a lendable portable disk (BrainBall) device and the ability to
+receive extremely large datasets directly on LTO8 tape.
+* Provide download access to all public datasets.  Current supported
+download methods include Globus and FTP.
+* Provide project-only access to brain-initiative collaborations, allowing
+collaborators to share and operate on datasets prior to publication.
 * Provide stable DOIs that can be used in published literature to reference
-  specific datasets or images
+specific datasets or images.
+* Provide computational resources on which users can run applications that
+operate directly on BIL-housed datasets.
+* Host custom portals that can operate directly on BIL-housed datasets.
+* Collaborate with investigators on establishing standardized formats,
+pipelines, and services that can be adopted and/or made available through
+BIL.
 
-* Provide computational resources (such as VMs) on which users can run
-  applications that operate directly on BIL-housed datasets
 
 ## Out-of-scope
-* Performing registration or other analyses of datasets (though we do
-  supply resources for users to do this themselves)
+* Performing analyses for users (e.g. registration or other analyses of
+datasets)
 
 
 # Communication
+## Help Desk
+For technical questions, assistance depositing files in BIL including
+networking support, assistance retrieving data deposited in BIL or to comment
+on our Web documentation.
+
+Non-time critical issues:
+Submit a help ticket. Send email to [email protected]
+
+Time-critical issues:  
+Phone the PSC hotline at: 412.268.6350
+
+
 ## E-mail
-  Inquiries should be sent to [email protected]
+Please use [email protected] for any Brain Image Library issues or
+questions in lieu of contacting specific people listed.
+
 
 ## Website
-  http://www.brainimagelibrary.org/
+Informational website containing instructions and current inventory:  
+http://www.brainimagelibrary.org/
 
+Restricted-access authenticated submission portal for all submissions to BIL:  
+http://submit.brainimagelibrary.org/
 
-## Funding
-Link to the NIH Reporter link or appropriate reference
-[pending]
+The BIL is operated as a partnership between the Biomedical Applications
+Group at the Pittsburgh Supercomputing Center, the Center for Biologic
+Imaging (CBI) at the University of Pittsburgh, and the Molecular Biosensor and
+Imaging Center at Carnegie Mellon University:  
+http://www.psc.edu/  
+http://www.cbi.pitt.edu/  
+http://pathways.mbic.cmu.edu/  
 
+## Funding
+The Brain Image Library is supported by the National Institutes of Mental
+Health of the National Institutes of Health under award number R24-MH-114793.
+[NIH Reporter Link](https://projectreporter.nih.gov/project_info_description.cfm?aid=9737988&icde=47261137&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=)