Submitting image data to BioStudies

1. You will need a BioStudies account. You can sign up here: https://www.ebi.ac.uk/biostudies/submissions/#/signup. Or, follow the link from Submit on the BioStudies homepage.
2. Prepare your raw data. Ideally your raw image files will be contained in a single directory with a logical hierarchical file structure.
3. To upload image files into your BioStudies account, go to the Files area in the BioStudies submission tool. If you have a smaller number of files (e.g., processed data files), you can use web upload - click on "Upload Files". For uploading large data volumes please use FTP or Aspera file transfer - instructions and the path to use are available under "FTP/Aspera" button; instructions are also below.

4. You will need a "table of contents" for your image files, called a "File List" in the submission tool. The purpose of this file is to provide information about the individual image files that will help the users of your dataset understand what different files mean and under what conditions they have been acquired. It can be a tab delimited file (in which case file extension should be ".tsv"), or an Excel file (".xls" or ".xlsx").

   The first line is a header line, and the first cell has to contain word "Files". Headers for the other columns are not predefined; we recommend to use descriptive, self-explanatory names. In future we expect this to be better standardized so that file lists could be parsed by a machine. Some examples of column headers: Compound, Concentration, Time (for compound treatment experiments), Gene (for genetic variation studies), Plate, Well, Field (for high content screening studies), Channel, Description, QC info. It is useful to include only attributes that have at least two distinct values for the set of image files you are describing in a particular file list; include constant values (e.g., "Organism") in the annotation of the study entered via the web form.

   Use as many lines as there are files in your dataset, and enter the exact filenames in the first column. Note that filenames are case-sensitive. If you have organized files in your BioStudies home directory in a hierarchy, do not forget to reflect that in the file list. E.g., if you have in your home directory folders "ExperimentA" and "ExperimentB", refer to files inside those folders as "ExperimentA/imageFile1.tif" etc. Fill in attribute values for each of the image files. Do not leave blank lines.

5. When all image files and one or more file lists have been uploaded, go to the "Submissions" section in the submission tool and click "Add new"; select "BioImages" from the list to create an image dataset. Fill in all the necessary fields in the web forms that will be offered, and make sure that the validation panel on the left indicates "all ok". When that is the case, click on "Submit". Your submission will be loaded into the BioStudies database and assigned a unique BioStudies accession number (i.e., dataset identifier); details on how to access and share your study with others will be available in a confirmation window, as well as in an e-mail.

Uploading Files using FTP and Aspera

BioStudies submitters can use the BioStudies Submission Tool web application for uploading data file. However, for large information volumes (i.e., number and/or size of files) this is not practical. This is particulaly applicable for image studies. Therefore, FTP and Aspera can be used for uploads. You will need to know your secret directory name to be able to upload data into your BioStudies ‘Files’ area.

FTP uploads

The FTP server is ftp-private.ebi.ac.uk, FTP user is ‘bsftp’, and the password is ‘bsftp1’. Use any FTP client such as FileZilla, or issue FTP commands via a command line, e.g.,

    ftp ftp-private.ebi.ac.uk
    Name: bsftp
    Password: bsftp1
    ftp> cd 78/348482-52fd-4ade-9273-bdeac6d93423-a116 (this is an example of the secret key directory name)
    ftp> put testFile
    

Aspera uploads

Aspera ascp command line interface can be downloaded here: aspera cli. Please select the correct operating system. The ascp command line client is present in the bin folder in the installation directory.

Your command for upload should be like this:

    ascp -P33001 -i <key> -d <local directory to upload> bsaspera_w@hx-fasp-1.ebi.ac.uk:.dropbox/<secret directory name>

• -P33001 and bsaspera@fasp-beta.ebi.ac.uk defines the port, user and server for the Aspera connection
• -d tells the server to create the directory if it does not yet exist
• <key> is the public key for the Aspera connection which has the value <aspera cli installation directory>/etc/asperaweb_id_dsa.openssh for Linux/MacOS and <aspera cli installation directory>\etc\asperaweb_id_dsa.openssh for Windows.
• <secret directory name> looks like this: 12/348482-5ded-45de-9273-badec6d93423-a111

Finding and accessing data

Please see the BioStudies help page to learn how to search and download data.