Platform for Drug Discovery


Data_upload


Table of contents


Create a project


  1. Click 'Project' tab at the top.
    • Image
  2. Click 'Create New Project' button.
    • Image
  3. Fill information about this project.
    • Image
    • All items are only used for recognition from users.
  4. Click 'close' button. This is the end of the project creation.
    • Image

Upload data to a project (for small data via HTTPS)


  1. Click a project ID of a project on which you want to upload the data from the project list in the project tab.
    • Image
  2. Click 'Upload My Data' button.
    • Image
  3. Click 'Upload via HTTPS' button.
  4. Fill an entry column for a 'Data Label'.
    • Image
    • This 'Data Label' is used for identification of the data.
    • A short name is recommended to set. Text area for these labels of a data icon in a 'Project - Detail' displays only the first 10 characters. So a name longer than 10 characters are difficult to distinguish.
    • Image
      An image of a data icon in a 'Pipeline - Detail' view
      Only the first 10 characters '1234567890' is displayed usually.
      When you focus a mouse cursor on the icon, a tooltip of the full sentence label is displayed.
  5. Choose a dataset type from a list.
    • Image
    • Choose dataset type precisely, because our system choice the executable pipelines according to this dataset type. You cannot choose data as an input for a pipeline with a wrong dataset type which the pipeline developer do not intended. In addition, if you choose the wrong dataset type which does not match the data, executed pipelines will stop with unexpected 'Abort' status, or will return unexpected result data in despite of with normal 'End' status.
  6. Choose an upload file from your computer.
    • Image
    • Basically, number of uploadable file is only 1 except cases described below. If you have some lanes of sequences from a sample and you want to merge them, please upload these sequences per a lane and run a merge pipeline.
    • Some dataset type like 'fastq(paired-end)' or 'csfasta+qual(single-end)' require to upload specific number of files, or allow to upload multiple files. You can choose two or more files after you push 'Add file' button.
    • Note that the expected number of file and file types are described in the dataset type specification page.
  7. You can optionally fill 'Optional Information' below the 'Upload' button for data recognition. You can freely edit this information after uploading.
    • Image
    • ‘Application Type' is sometimes used initial format choice of viewing in our genome viewer, Genome Explorer. For instance, when you choose 'Bisulfite-Seq' as 'Application Type', the mapped result is loaded modified base mode as a default.
    • 'Organism' is used for auto choice of a genome in mapping or loading data to a viewer.
  8. Click 'Upload' button after you fill required information and choose upload target files.
    • Image
  9. Please wait several minutes for uploading small data, or wait several hours for uploading huge data.
    • Image
  10. Click 'Open Project Detail window' button. This is the end of the data uploading via HTTPS.
    • Image
  11. Please confirm uploaded data icon is displayed in the 'Project - Detail' view.
    • Image

Upload data to a project (for huge data via SFTP)


  1. Click a project ID of a project on which you want to upload the data from the project list in the project tab.
    • Image
  2. Click 'Upload My Data' button.
    • Image
  3. Click ‘Upload via SFTP’ button.
  4. Installation and uploading with the specific data transport application.
  5. Click 'Open your folder on the server' button to confirm uploaded data
    • Image
  6. After confirmation uploaded data, click 'Next' button.
    • Image
  7. Fill an entry column for a 'Data Label'.
    • Image
    • This 'Data Label' is used for identification of the data.
    • A short name is recommended to set. Text area for these labels of a data icon in a 'Project - Detail' displays only the first 10 characters. So a name longer than 10 characters are difficult to distinguish.
    • Image
      An image of a data icon in a 'Pipeline - Detail' view
      Only the first 10 characters '1234567890' is displayed usually.
      When you focus a mouse cursor on the icon, a tooltip of the full sentence label is displayed.
  8. Choose a dataset type from a list.
    • Image
    • Choose dataset type precisely, because our system choice the executable pipelines according to this dataset type. You cannot choose data as an input for a pipeline with a wrong dataset type which the pipeline developer do not intended. In addition, you choose the wrong dataset type which does not match the data, executed pipelines will stop with unexpected 'Abort' status, or will return unexpected result data in despite of with normal 'End' status.
  9. Choose an uploaded file in your directory in our server.
    • Image
    • If the file list is empty, please back to this step.
    • Note that the directory for uploading is shared with your group members. Most of users join in a lonely group, this is not concerned.
    • Basically, number of uploadable file is only 1 except cases described below. If you have some lanes of sequences from a sample and you want to merge them, please upload these sequences per a lane and run a merge pipeline.
    • Some dataset type like 'fastq(paired-end)' or 'csfasta+qual(single-end)' require to upload specific number of files, or allow to upload multiple files. You can upload two or more files at once and check them on your uploaded file list.
    • Note that the expected number of file and file types are described in the dataset type specification page.
  10. You can optionally fill 'Optional Information' below the 'Upload' button for data recognition. You can freely edit this information after uploading.
    • Image
    • ‘Application Type' is sometimes used initial format choice of viewing in our genome viewer, Genome Explorer. For instance, when you choose 'Bisulfite-Seq' as 'Application Type', the mapped result is loaded modified base mode as a default.
    • 'Organism' is used for auto choice of a genome in mapping or loading data to a viewer.
  11. Click 'Upload' button after you fill required information and choose upload target files.
    • Image
  12. Please wait a few second for moving the upload directory to a data storage directory.
    • Image
  13. Click 'Open Project Detail window' button. This is the end of the data uploading via SFTP.
    • Image
  14. Please confirm uploaded data icon is displayed in the 'Project - Detail' view.
    • Image

Difference between HTTPS and SFTP


  • Both HTTPS and SFTP is a data transport secure protocol via the Internet.
  • Following table shows the difference between the two.
#pointHTTPSSFTP
1Available data sizeDepend on the internet environment
Sometimes less than 1 gigabyte
Can operate huge data
(More than several gigabytes)
2A required application for transportationWith common web browserSpecific tool or command
3FeatureEasy to use
Automatically a web browser transports in this protocol
Frequently fail to transport huge data
Usually success to transport huge data in an instable network