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Uploading using the Java GUI
There are two basic features to the ProteomeCommons.org Tranche netowork: adding data and getting data. This document discusses how the average user adds data to the Tranche network. If you are interested in information about using the command line tool or creating your own custom tool using Java, view the Developer's upload information page.
This page is broken in to the following sections. You can either read the page from top to bottom, or you can skip directly to the section of interest.
How to upload data to Tranche
Files can be added to the network using a point-and-click style tool, often refered to as the Java Graphical User Interface (GUI). The tool is intended to be straight-forward to operate by anyone who wants to manually upload a file or a directory of files. In order to use this tool, you must have a copy of the files to be uploaded on your local computer, and you must have permission to upload to the network. If for any reason you need help with the upload process, please post a message on the Tranche users group.
You will need an account to upload to the Tranche Network. If you do not already have an account, visit How to Apply for an Account.
Launch the main Tranche tool to start a new upload. This is the "Launch Tranche" link on the Tranche Homepage. Click here to launch the tool directly from this page. The tool should look like the following.
Normally the @buildNumber will be replaced with the current Tranche build, as listed on the on the Tranche Homepage. If these numbers do not match, close the Tranche tool, clear your web browser's cache, and re-launch the Tranche tool.
Next, login by clicking on the "Log In" link in the top right-hand corner of the Tranche tool. You'll be prompted for the location of your Tranche user file and you will have to enter your password. Once you've logged in your user name will appear in the top right-hand corner. After logging in, click on the "Servers" tab to verify that you have upload permission.
You should notice that the "Read-Only" next to the server names will switch to something like "Read/Write" or "Admin" based on your user status. This means you can upload data. Please note the following special instructions for current data uploads while the Tranche servers are being upgraded.
Confirm that there are servers selected by clicking on the "Configuration" menu item in the top-left of the screen. The advanced configuration screen will appear showing that there are servers selected.
While the configuration screen is present, it is also a good time to enter a passphrase if you'd like to encrypt the uploaded data. This is optional. If used, the data will only be accessible to people who you share the entered passphrase with. When finished click on the "Save Changes" button.
Enter the remaining information in the upload screen. This includes the file or directory that you'd like to upload, a title, and a description of the upload. When complete the screen should look similar to the following.
Finally, click on the "Upload File(s)" button to upload the data. An exact copy of the file or directory selected will be uploaded, including any sub-folders and sub-folders of those, etc. You will be able to monitor upload progress by watching the "Upload" tab in the main Tranche tool.
A confirmation message will appear once the upload completes. This message will give you the option to e-mail information related to the upload to your e-mail address. It is recommended that you do this in order to more easily remember the Tranche hash for your upload. This hash is what you should cite so that others can download the data.
Note that the hash listed above is a valid hash. If you'd like to test downloading a project, you can use the hash shown above:
Upload Tips
Here are a few tips to consider when uploading data to Tranche.
- Do not compress your files in to a ZIP or tar ball (tar.gz) format. Upload a plain uncompressed directory of your files. Tranche will automatically compress the files and group them together for you. Additionally, uploading files individually allows you, and users, to download and use subsets of files.
- Do not worry about uploading too large of a file or too many small files. Tranche is very good at handling both of these cases. It is preferred that you simply upload the data in the form that it comes from your acquisition software, i.e. a few large .raw files or a large directory of .dta files.
- Tranche will automatically skip uploading files that are already on the network. If an upload is stopped/interrupted prior to completion, you can resume the upload by simply restarting the upload. The portions of the upload that are already on-line will not be uploaded a second time.
- If you are uploading lots of data, you should group it in smaller, logical chunks. By doing this you will have several small uploads, each with a unique hash string. You can use these hash strings to more easily download, backup, or do anything else you like with the data.
- Feel free to rearrange and upload the same data as many times as you want in order to make convenient downloads. Tranche is smart enough to reuse uploaded data. For example, you might upload an entire project, then reupload just the peak lists, then reupload just the raw spectra. This would make 3 different hash strings that you could provide to let users download everything, just the peak lists, or just the raw data.