Synapse helps you organize your uploaded data in an efficient way.
Projects
Projects in Synapse are “containers” that group relevant content and people together. All data must be uploaded into a project. Projects can be private so only you can see the contents, they can be shared with your collaborators, or they can be made public so anyone on the web can view your research.
Projects help you to:
Organize your work: With Synapse you can organize the parts in your workflow (data, code, etc) into a hierarchy like a file system. With the tabs across the top of each project, you can easily navigate to your wikis, files and folders, SQL-based tables, and even conduct conversations using discussion forums.
Store data, code, and results: You can upload your data, code, and results to Synapse, or store a reference to their location in your local computer system or on the web. Everything can be stored as files hosted by Synapse, in your own external cloud storage, or using Docker containers.
Control data access or release it publicly: You have complete control over how users and groups can interact with your work. Work privately, openly, or somewhere in between.
Link and share content with others: Just as you can control the access to your work, projects can serve as a platform for linking and sharing your work with others.
Custom, searchable annotations: Assign any key/value pair you want. Those values become searchable and available to those granted access.
Attach figures and documents: Upload documents and images via the website or programmatically.
Creating a Project
To create a new project:
Navigate to your Synapse Dashboard and click on the Projects tab.
Click the Create a New Project button.
Decide on a unique name for your Project and click Save.
Files
Synapse files can be created by uploading content from your local computer or linking to digital files on the web. You can annotate files with custom metadata, embed files into Synapse wiki pages, or associate them with a /wiki/spaces/DOCS/pages/1972405096. Files in Synapse always have a “parent”, which could be a project or a folder. You can organize collections of files into folders and sub-folders, just as you would on your local computer.
Synapse files (as well as folders and projects) are identified by a unique identifier called a Synapse ID, or synID. The synID is represented by the prefix “syn” followed by numbers (for example, syn12345678). This identifier can be used to refer to a specific file on the web and through the programmatic clients.
You can control who has access to files that you upload in two ways. First, you can apply sharing settings, which are permissions that control who can view, edit, download, or delete a file. Second, you can also apply conditions for use, which are additional requirements that Synapse users must meet before accessing your file. By default, files inherit the conditions for use of the Synapse folder where they are uploaded. You can also add additional conditions for use on specific files within a folder. To read more about how to use sharing settings and conditions for use together, see the Sharing and Accessing Data page.
Folders
Folders offer an additional way to organize your data. Instead of uploading a bunch of single files into your project, you can create folders to separate your data in a systematic way. You can create a folder within a folder within a folder, and so on.
Creating a Folder
To create a folder:
Within your Synapse project, click the Files tab
To create a folder at this level*, click the Files Tools menu, followed by Add New Folder
Enter a folder name and click Save
*To create a folder within a folder, click on the folder name within the project, and click the Folder Tools menu, followed by Add New Folder, and proceed to step 3.
Uploading a File via the Synapse UI
To upload a file:
Within your Synapse project, click the Files tab
Click the Files Tools menu (or, to upload a file to a folder, then first go to the folder, and click the Folder Tools menu), followed by Upload or Link to a File
Click Browse to select the file, or drag and drop it to upload, or click Link to URL to add a link to an external storage space
Click Save
Uploading a File Programmatically
You can annotate your data during the upload process or after. Find more information here.
Command line
The command line has the sub-command store, which can be used to upload and add a file to Synapse.
# Add a local file to an existing project (syn12345) on Synapse synapse store raw_data.txt --parentId syn12345
Python
The main function for uploading or updating a file in the Python client is through the store function. For more information about this function, see the Python Docs.
import synapseclient from synapseclient import File syn = synapseclient.login() # Add a local file to an existing project (syn12345) on Synapse file = File(path='/path/to/raw_data.txt', parent='syn12345') file = syn.store(file)
R
The main function for uploading or updating a file in the Python client is through the synStore function. For more information about this function, see the R Docs.
library(synapser) synLogin() # Add a local file to an existing project (syn12345) on Synapse file <- File(path='/path/to/raw_data.txt', parentId='syn12345') file <- synStore(file)
Moving a File or Folder via the Synapse UI
Using the Synapse UI, you can move single files one at a time, or you can move entire folders containing many files. You cannot move batches of files (more than one folder) at once. For this reason, if you are primarily using the web interface to manage your files, you should consider your folder structure carefully when you create your initial project.
To move a file or folder:
Within the file or folder, click File Tools or Folder Tools, followed by Move File or Move Folder
In the resulting pop-up window, browse for the destination folder or project or use the search bar to enter the Synapse ID of the new location
Moving a File or Folder Programmatically
Command line
The command line client has a sub-command mv which can be used to move files and folders.
# move a file or folder (syn123) to a different folder/project (syn456) synapse mv --id syn123 --parentId syn456
Python
You can change the file or folder location in the Python client by fetching the file information, changing the parent property, and storing the change.
import synapseclient
syn = synapseclient.login()
# fetch the file/folder to move (syn123 in this example)
# note the downloadFile=False parameter to fetch only the file's metadata and not the entire file
foo = syn.get('syn123', downloadFile=False)
# change the parentId to the new location, can be a folder or project (syn456 in this example)
foo.properties.parentId = 'syn456'
# store the file/folder to move it
syn.store(foo)
R
You can change the file or folder location in the R client by fetching the file information, changing the parent property, and storing the change.
library(synapser)
synLogin()
# fetch the file/folder to move (syn123 in this example)
# note the downloadFile=False parameter to fetch only the file's metadata and not the entire file
foo <- synGet('syn123', downloadFile = FALSE)
# change the parentId to the new location, can be a folder or project (syn456 in this example)
foo$properties$parentId <- 'syn10056031'
# store the file/folder to move it
synStore(foo)
Deleting a File or Folder via the Synapse UI
Deleting a file will permanently remove it from Synapse. The synID that was associated with the deleted file will not be re-used. To delete a file:
Within the project, click the Files tab
Click the file or folder you want to delete (or the file/folder within a folder)
Click File Tools or Folder Tools, followed by Delete File or Delete Folder
Deleting a File or Folder Programmatically
Deleting a file will permanently remove it from Synapse. The synID that was associated with the deleted file will not be re-used.
Command line
synapse delete syn56789
Python
import synapseclient
syn = synapseclient.login()
entity = syn.delete("syn56789")
R
library(synapser)
synLogin()
entity <- synDelete("syn56789")
File Previews
Synapse has a viewer for certain file types so that you can preview them before you download. Synapse previews will show the contents of the following file types:
PDFs
CSV (may show a portion of the table only)
Videos (.mp4, .webm, .ogg)
Jupyter notebooks (.ipybn)
Images (.jpeg, .png, .gif, .svg)
HTML (limited rendering only)
Markdown (.md or .rmd)
To see a file preview, navigate to the Files tab of a project and click on the file name. If a file preview is available, it will be visible in the left window.