updated DRC info

_data/sidebars/sparc_sidebar.yml

@@ -12,18 +12,21 @@ entries:
     - title: Information
       url: /introduction.html
       output: web, pdf
+    - title: DRC Resources and accounts
+      url: /user_accounts.html
+      output: web, pdf  
     - title: Contributing to the documentation
       url: /doc_contribute.html
       output: web, pdf
-  - title: Data submission
+  - title: Submitting Data 
     output: web, pdf
     folderitems:
-    - title: User accounts
-      url: /user_accounts.html
-      output: web, pdf  
-    - title: Submitting data
+    - title: Data curation steps
       url: /submit_data.html
       output: web, pdf
+    - title: Uploading files
+      url: /file_upload_dat_core.html
+      output: web, pdf
   - title: DAT-Core Information
     output: web, pdf
     folderitems:

pages/dat_core/dat_core_roadmap.md

@@ -25,6 +25,7 @@ This document outlines the SPARC milestones for the DAT-Core as outlined in the
 3. **Support for dataset status:** Adding support for a status flag on datasets indicating the stage of curation it is in (draft, in-review, finalized)
 4. **Support for N-dimensional imaging data:** The DAT-Core will expand functionality for 3D clinical imaging, and N-Dimensional microscopy imaging. 
 5. **Improved tracking of SPARC data-use:** The DAT-Core will improve funcitonality to track how much data is contributed by SPARC investigators.
+6. **Support for two additional file formats:** The DAT-Core will add support for 64-bit Spike2 files and .ac2 files.
 
 ### Q3: April-June 2019
 
@@ -40,6 +41,7 @@ This document outlines the SPARC milestones for the DAT-Core as outlined in the
 1. **Support for hierarchical ontologies:** The DAT-Core will expand functionality to link to ontologies and support for hierarchical ontologies. 
 2. **Support for merging metadata from multiple datasets:** The DAT-Core will provide functionality to merge metadata between datasets.
 3. **Expanded support for the Open Data Library:** DAT-Core will implement functionality to allow investigators outside the SPARC initiative, without a subscription to the DAT-Core platform, to access/download data from the Open Data Library in a sustainable way (cost for downloading data will be passed ot the downloader).
+4. **Support for two additional file formats:** Specific file formats are TBD.
 
 
 ### SPARC Year 3

pages/dat_core/file_upload_dat_core.md

@@ -0,0 +1,19 @@
+---
+title: "Uploading files to the DAT-Core"
+keywords: documentation, github
+sidebar: sparc_sidebar
+permalink: file_upload_dat_core.html
+summary: This page outlines the various ways that files can be uploaded to the DAT-Core. 
+folder: general
+---
+
+
+## Introduction
+SPARC investigators are required to upload their scientific files to the DAT-Core. There are multiple ways for users to upload files to the platform. Here, we describe the various options and provide links to tutorials describing step by step instructions to upload files.
+
+Please see the [Blackfynn Help](http://help.blackfynn.com) for more information.
+More SPARC specific information soon:
+
+
+
+

pages/data_submission/dat_core_user_accounts.md

@@ -1,30 +1,36 @@
 ---
-title: "User Accounts"
+title: "User Accounts & Organizations"
 keywords: documentation, github
 sidebar: sparc_sidebar
 permalink: user_accounts.html
-summary: This pages outlines the workflow for submitting data to the SPARC DAT-Core. 
+summary: This page describes the various accounts and resources that are available to the SPARC investigators.
 folder: general
 ---
 
-## User accounts on the DAT-Core
+## Organizations on the DAT-Core
 
-All SPARC investigators have access to the DAT-Core platform ([Blackfynn](https://app.blackfynn.io)). SPARC Investigators will have access to two accounts on the Blackfynn platform. 
+All SPARC investigators have access to the DAT-Core platform ([Blackfynn](https://app.blackfynn.io)). SPARC Investigators will have access to two organizations on the Blackfynn platform. 
 
-1. **A private account for their lab:** This account is available to the individual SPARC investigators and is independent of the SPARC requirements. Investigators can use this account for their data management needs within, and beyond the SPARC program. This account is private and not managed by the SPARC Consortium and has the same restrictions as a standard [Blackfynn academic subscription](https://www.blackfynn.com/academia)
+1. **A private organization for their lab:** 
+These accounts will should no longer be used for SPARC related efforts and will be transitioned to our standard free academic subscription model by March 2019 ([Blackfynn academic subscription](https://www.blackfynn.com/academia)). The private lab accounts were created for individual labs during the first year of the DAT-Core effort. However, starting in December 2018, all SPARC related data should be hosted in the **SPARC Confidential** organization. 
 
-2. **The SPARC Consortium account:** This account will be used for all data submissions to the SPARC consortium. This account will enforce strict data models and data submission processes. 
+2. **The SPARC Confidential organization:** 
+This organization will be used for all data submissions to the SPARC consortium. Investigators can create private datasets in this organization, and selectively share their dataset within this organization with other individuals or teams.  
 
-The remainder of the SPARC documenentation will reference the **SPARC Consortium organization** only. 
+For the remainder of the SPARC documenentation, any notion of organization on the DAT-Core will reference the **SPARC Consortium** organization only. 
 
-### The SPARC Consortium account on the DAT-Core
+### The SPARC Confidential organization on the DAT-Core
 
-Since the SPARC Consortium account will host all SPARC data (including embargoed data), access to to this organization will be restricted until users sign a non-disclosure agreement (NDA). User accounts to this organization will be managed by the DAT-CORE. By signing the NDA, SPARC awardees agree not to unilaterally publish or disseminate data made available from other labs and not to use data for commercial purposes during the embargo period. Once the users have signed the NDA, they will be granted access to the SPARC Consortium account. 
+Since the SPARC Confidential organization will host all SPARC data (including embargoed data), access to to this organization will be restricted until users sign a non-disclosure agreement (NDA). User accounts to this organization will be managed by the DAT-CORE. By signing the NDA, SPARC awardees agree not to unilaterally publish or disseminate data made available from other labs and not to use data for commercial purposes during the embargo period. Once the users have signed the NDA, they will be granted access to the SPARC Consortium account. 
 
 ### SPARC Teams on the DAT-Core
 
 Once users are accepted into the SPARC Consortium account, each investigator group can create a team. Initially, teams will reflect the individual laboratories, but it is possible to create any number of teams comprised of SPARC investigators (i.e. users with access to the SPARC Consortium Account). Teams will be used to set data access rights and roles for submitted datasets.
 
 ## SPARC Slack Organization
 
-All SPARC investigators can join the SPARC [Slack Account](https://www.slack.com). SPARC uses Slack to foster collaboration and communication between investigators within the SPARC program. If you are interested to join the Slack account, send a message to Leonardo Guercio from the DAT-Core ([email protected]).
+All SPARC investigators can join the SPARC [Slack Account](https://www.slack.com). SPARC uses Slack to foster collaboration and communication between investigators within the SPARC program. If you are interested to join the Slack account, send a message to Leonardo Guercio from the DAT-Core ([email protected]).
+
+## SPARC TalentLMS
+
+SPARC is using [TalentLMS](https://learnwithsparc.talentlms.com/index) for documentation, tutorials and resources related to SPARC meetings. Please contact Sue Tappan from MBF for more information.

pages/data_submission/submit_data.md

@@ -1,5 +1,5 @@
 ---
-title: "SPARC Data submission workflow"
+title: "SPARC Data curation steps"
 keywords: documentation, github
 sidebar: sparc_sidebar
 permalink: submit_data.html
@@ -14,8 +14,10 @@ folder: general
 
 ### Creation of a draft dataset
 **Timeline:** Creation of a draft dataset is up to the investigator 
-Who has access to the data: The data is private and is accessible only to those that you specifically invite to access the data (this applies to the DAT-Core as well).
-Who owns the data: The investigator that submitted the data or the person who is assigned as the owner of the dataset.
+
+**Who has access to the data:** The data is private and is accessible only to those that you specifically invite to access the data (this applies to the DAT-Core as well).
+
+**Who owns the data:** The investigator that submitted the data or the person who is assigned as the owner of the dataset.
 
 **Process:** At any time, users can create a draft dataset within the SPARC Consortium account in preparation for submitting the data to the consortium. 
 
@@ -24,36 +26,42 @@ At this time, the data is private to the data owner. At any point in time, users
 **Required steps for the data owner:**
 - Creating and naming a dataset (see: Creating datasets )
 - Providing a description of the dataset
-- Selecting the SPARC data models that are applicable to the data that is being submitted.
-- Uploading files and annotating the data with the data standards models as seen fit. (see: Uploading data and Annotating data with records )
+- Uploading files and annotating the data as preparation for the data curation team.
 
+### Sharing draft dataset with the data curation team
+**Timeline:** Sharing the data with the data curation team is up to the investigator
 
-### Initial submission and publishing as embargoed dataset
-**Timeline:** Finalizing the draft dataset is required 1 month after the completion of a data milestone
-Who has access to the data: The data is now shared with the SPARC Consortium and all SPARC investigators can see the data.
-Who owns the data: The investigator that submitted the data or the person who is assigned as the owner of the dataset.
+**Who has access to the data:** The data is private and is accessible only to those that you specifically invite to access the data. At this stage this will include the data curation team.
 
-**Process:** At a specific point in time when a data milestone is due, the NIH Leadership team will require the investigators to share the draft dataset with the SPARC Consortium. The dataset is now considered to be an embargoed dataset. 
-Making the data available to the SPARC consortium will provide “read-only” access to all members of the SPARC Consortium account. The investigator is still the data owner and is the only member who can change who can edit the data in the dataset. 
+**Who owns the data:** The investigator that submitted the data or the person who is assigned as the owner of the dataset.
+
+**Process:** The data curation team will work with the investigators to curate the dataset. This includes capturing the metadata and mapping it to the standardized models developed by the data standards committee.
 
 **Required steps for the data owner:**
-- The owner will have to change the ‘sharing’ setting to include the entire SPARC Consortium account. 
+- Share the dataset with the SPARC curation team on the DAT-Core platform
+- Work with the curation team to curate the data
+
 
-### Finalize submission and integration in SPARC Resource
-**Timeline:** We expect that the metadata curation team will work with the SPARC team over a period of a month to ensure that the dataset adheres to the SPARC data standards.
-Who has access to the data: The data is shared with the SPARC Consortium and the data curation team will work with the investigators to finalize the dataset.
-Who owns the data: The investigator that submitted the data or the person who is assigned as the owner of the dataset
+### Initial submission and publishing as embargoed dataset
+**Timeline:** Finalizing the draft dataset is required 1 month after the completion of a data milestone
 
-**Process:** After data is made available to the SPARC consortium as an embargoed dataset, the metadata curation team will start validating the submitted dataset and work with the data owners to make sure the submitted dataset adheres to the required data standards. In addition, the metadata curation team will initiate integration of the data into the SPARC Integrated Dataset. 
+**Who has access to the data:** The data is now shared with the SPARC Consortium and all SPARC investigators can see the data.
+
+**Who owns the data:** The investigator that submitted the data or the person who is assigned as the owner of the dataset.
+
+**Process:** At a specific point in time when a data milestone is due, the NIH Leadership team will require the investigators to share the draft dataset with the SPARC Consortium. The dataset is now considered to be an embargoed dataset. 
+Making the data available to the SPARC consortium will provide “read-only” access to all members of the SPARC Consortium account. The investigator is still the data owner and can restrict who has 'edit' permissions on the dataset.
 
 **Required steps for the data owner:**
-- Work with the curation team to ensure the dataset adheres to the data standards.
+- The owner will have to change the ‘sharing’ setting to include the entire SPARC Consortium account with read-only priviledges.
 
 
 ### Publishing submitted dataset into public domain 
 **Timeline:** One year after the initial submission of the dataset.
-Who has access to the data: The dataset is now publicly available. There will be processes that require people outside the SPARC Consortium to request access to the data from the data owner. 
-Who owns the data: The investigator that submitted the data or the person who is assigned as the owner of the dataset.
+
+**Who has access to the data:** The dataset is now publicly available. There will be processes that require people outside the SPARC Consortium to request access to the data from the data owner. 
+
+**Who owns the data:** The investigator that submitted the data or the person who is assigned as the owner of the dataset.
 
 **Process:** One year after the the creation of the embargoed dataset, the data owner will be required to make the dataset public on the Open Data Library. When datasets are shared publicly, the data will receive a DOI which can be used to reference the data in publications.