Upload files to dat-core information

pages/dat_core/file_upload_dat_core.md

@@ -11,9 +11,79 @@ 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:
+## Step 1: Creating a dataset
+All files belong to a dataset on the DAT-Core platform. A dataset contains both files and metadata and can be selectively shared with other users of the platform. You can create datasets through the web application or using one of the [client tools](https://developer.blackfynn.io). Click [here](http://help.blackfynn.com/blackfynn-web-application/importing-and-managing-data/creating-and-deleting-datasets) to see more detailed information on how to create datasets on the DAT-Core platform.
 
+## Step 2: Uploading files
+Once you have created a dataset, you can upload files to this dataset. You can create folders to separate files in a logical structure. After files are uploaded, you can associate files with metadata records. There are number of ways to upload files:
+
+### Upload files using the browser
+Within a dataset, you can navigate to the 'Files' tab. This is the main location where all files are organized. 
+
+{% include image.html file="dat_core_file_tab.png" alt="file upload" %}
+
+In the 'Files' tab, you can create folders to organize your files on the platform. Click on the "New Folder" button to create a new folder. You can navigate into a folder by clicking on the folder in the file browser.
+
+To upload files, you can drag files from your local machine directly into the file browser panel. A popup window will show the files that will be uploaded. Note that two of the files in the example below are combined as they belong to the same timeseries package.
+
+{% include image.html file="dat_core_upload_modal.png" alt="file upload" %}
+
+Click 'Start Upload' to begin uploading the files. During the upload process, you can safely hide the popup window as files will continue to be uploaded in the background. Once files are uploaded to the platform, they will show up in the file browser. 
+
+Depending on the file format, the platform will process the data to enable the data to be viewed in the browser based data viewer. Processing of the data can take a while and you will be notified when this has completed.
+
+For more information, see the [File Upload Documentation for Blackfynn](http://help.blackfynn.com/blackfynn-web-application/uploading-files-to-a-dataset) 
+
+### Upload files using the Blackfynn Agent
+The Blackfynn Agent is a command line interface (CLI) that is available for Windows, Linux and Mac OS. It allows users to interact with the platform programmatically using the command line. The Blackfynn Agent is currently in Beta and will over time replace the Python based CLI. 
+
+To upload data using the Blackfynn Agent you will have to first install the agent. After installing and configuring the tool, you can upload files using the ```upload``` command. 
+
+```bash
+./blackfynn_agent upload ~/Desktop/ --dataset {datasetId}
+``` 
+
+Tutorials on how to install and configure the agent, as well as how to upload data using the agent can be found in the [Blackfynn Developer documentation](https://developer.blackfynn.io/agent/) for the CLI.
+
+### Upload files using Python
+You can use the Open Source Blackfynn Python Library to upload files to the DAT-Core platform.  In Python, you will first need to import the library adn establish a connection to the platform. Then retrieve or create a dataset. The dataset object has a method to upload files to the dataset as the following example highlights.
+
+```python
+ # import Blackfynn
+ from blackfynn import Blackfynn
+
+ # create a client instance
+ bf = Blackfynn()
+
+ # create a dataset
+ ds = bf.create_dataset('Timeseries Dataset')
+
+ # upload data (3 files)
+ ds.upload('example_data/test.edf', 'example_data/testData.nev', 'example_data/testData.ns2')
+
+```
+
+More information can be found in the [Blackfynn developers documentation for Python](https://developer.blackfynn.io/python) and the sourcecode for the Python Library [here](https://github.com/blackfynn/blackfynn-python).
+
+### Upload files using MATLAB
+Finally, you can also upload files using the MATLAB client. The MATLAB client relies on the Blackfynn Agent to upload the files so you will have to both install the MATLAB client as well as the Blackfynn Agent. The ```upload``` command is a method of the ```BFDataset``` class and can be used as follows:
+
+```R
+>> bf = Blackfynn();
+>> ds = bf.datasets(1)
+
+BFDataset with properties:
+
+    description: 'This is a dataset for the second tutorial.'
+         models: [1×3 BFModel]
+          items: [0×0 BFBaseDataNode]
+           name: 'tutorial2'
+           type: 'DataSet'
+
+>> ds.upload('~/Downloads/example_data');
+```
+
+A detailed tutorial on how to upload data using MATLAB can be found in the [Blackfynn developers documentation for MATLAB](https://developer.blackfynn.io/matlab) and the sourcecode for the MATLAB client can be found [here](https://github.com/Blackfynn/blackfynn-matlab).
 
 
 

pages/data_submission/dat_core_user_accounts.md

@@ -8,29 +8,24 @@ folder: general
 ---
 
 ## 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 organizations 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 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 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.  
+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 Consortium** organization.
 
-For the remainder of the SPARC documenentation, any notion of organization on the DAT-Core will reference the **SPARC Consortium** organization only. 
+2. **The SPARC Consortium 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 SPARC Confidential organization on the DAT-Core
+For the remainder of the SPARC documentation, any notion of organization on the DAT-Core will reference the **SPARC Consortium** organization only.
 
-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. 
+### The SPARC Consortium organization on the DAT-Core
+Since the SPARC Consortium 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]).
 
 ## 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.
+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.