User Interface¶
There are two main interfaces where you can interact with GeoBiologics:
-
the Project Editor where you could submit jobs and view results interactively, and
-
the Control Panel for managing your projects, jobs, files, accounts, etc.
Project Editor¶
The project editor is composed of the a sidebar on the left and a main panel on the right.
The sidebar contains two panels:
- the New Job panel for viewing available job types and creating new jobs,
- the File & Job Manager panel for viewing and managing files and jobs in the current project.
The main panel contains one or more tabs, which can be categorized into:
- Structure viewer tab: Mol* Viewer for viewing biomolecular structures (this tab is always present and can not be closed),
- Job result tab: Job result panel for viewing the result of a job,
- Job submission tab: Job submission form for submitting a new job.
Sidebar¶
The sidebar is composed of three clickable components:
- The GeoBiologics logo. Clicking it will exit the current project and take you to the Control Panel.
- New Job panel for viewing available job types and creating new jobs. Clicking it while the panel is active will collapse the sidebar.
- File & Job Manager panel for viewing and managing files and jobs in the current project. Clicking it while the panel is active will collapse the sidebar.
File & Job Manager¶
In the "Files & Jobs" panel, you can view all the files and jobs of your project.
Press the 
button of a file/job entry to rename, copy the name of, delete or download the file/job.
- Protein structure files (.pdb, .cif) are shown with icon "
". Left click on a structure file to open it in the Mol* Viewer. - FASTA sequence files (.fasta) are shown with icon "
". Left click on a FASTA file to open it in a plain text viewer. - CSV tables (.csv) are shown with icon "
". Left click on a CSV file to open it in a table viewer. - Image files (.png) are shown with icon "
". Left click on an image file to open it in an image viewer. - Jobs are shown with icon "
" or "
" depending on whether it is expanded or collapsed. Left click on the icon to expand or collapse it. Left click on a job to view its Job Result.
If you want to filter the list of files and job, press the "
" button and select the filter conditions. You can filter the jobs by its job type, and choose whether or not imported/uploaded files will be shown. Click "Clear" to cancel all filter conditions.
To add a file to your project, simple hover over the "
" button and select the type of file you want to add in the dropdown menu. Available options include:
- Upload: Upload files of biomolecular structures from your local machine.
- Import from Cloud: Import a structure from PDB / AlphaFoldDB by entering the PDB ID or the UniProt ID.
New Job¶
In the "New Job" panel, you can view all available job types. Type in the search bar to search for job types that contain your specified keyword. Click on the icon of a job type to open the corresponding Job Submission Form.
Main Panel¶
The main panel contains one or more tabs, which can be categorized into Mol* Viewer, Job Result and Job Submission.
Click on the tab name to switch to the corresponding tab.
Tabs of the latter two types can be closed by hitting the "
" button.
On the top right of the main panel, you could open the Notification popover to see the latest messages by pressing the "
" button. If you need help, you could open this documentation by pressing the "
" button. If you click your avatar, you could log out, navigate to the Control Panel, or share your feedback with us.
Mol* Viewer¶
The Mol* Viewer is where you vividly visualize your biomolecular structures. It comprises three panels, the Sequence Viewer, the Structure Viewer and the Structure Objects panel. You can rotate, translate, zoom in/out, and select atoms, residues, and chains. You can also change the display style of the structure, such as the color, the representation, etc.
For a detailed tutorial on how to use the Mol* Viewer, please refer to the Using Mol* tutorial.
Job Submission Form¶
You can easily submit a job by filling out the job submission form. The form is divided into following three sections:
- Job introduction: Hover on the icon next to the form title (which is the job type) to view the description of the job and the required input formats. Please read it carefully to avoid errors.
- Job inputs: Here you can set the input(s) to the job. For the example here, you could either input the sequence in the text area or upload a FASTA file by pressing the "
" button. - Job parameters: Here you can set the models and the parameters of the job. Different models might have different parameters. Job parameters default state is hidden, you can click the "Show Parameters" text at the bottom of the form to show them.
After filling out the form, enter a name to identify this job and click the "Submit" button at the bottom-right to submit the job. If the job submission is successful, a toast saying "Job submission successful" will slide in from the top. If the job submission failed, a toast with the error message will appear instead.
After a job is successfully created, a new entry will be added in Files & Jobs.
The job entry will have a spin icon (
) when the job is pending or running.
Job Result¶
The job result panel is divided into the following sections:
-
Job Info: The job type, job status, run time, and the corresponding project name.
-
Input & Parameters: The input file(s) and parameter(s) of the job.
-
Summary Table: After the job finished, you would see a summary table of the job result. You can download the result by pressing the "
" button.
Control Panel¶
The control panel comprise the following pages: Project Page, Job Page, File Page, Account Page, and Support Page. You can navigate to these pages by clicking the corresponding item in the left sidebar.
To expand the main page on the right, press the "
" button to collapse the navigation sidebar. To restore the sidebar, press the same button again.
To log out of your account, hover over your avatar and click "Sign Out".
If you have any feedback to provide, hover over your avatar and click "Share your Feedback".
Project Page¶
Here is where you manage your projects.
At the top is a search bar you can filter your projects by name, by size and by last-modified date. Click "Reset" to reset the filter conditions. Click "Search" to initiate a search query. After a filtered search starts, a blue tag will appear for each filter condition, and the search results will be shown below. Click the icon of a tag to remove the filter condition.
The search results comprises project cards which displays the name, size and last modified time of your projects.
Click on a project card to enter the project editor and start designing / optimizing antibodies.
Hover above the project name and you will see a "
" icon. Click on it to rename the project.
Click on the "
" button to download all files within the project in a .zip file.
Hover above the "
" button to either
- List Files: get the list of files within the selected project. This will take you to the File Page.
- List Jobs: get the list of jobs within the selected project. This will take you to the Job Page.
- Delete: delete the selected project.
To perform batch operations, press the "
" button and click on the projects you want to select.
You can then perform batch operations on the selected projects by pressing either "List Files", "List Jobs", "Delete" or "Download".
To exit selection mode, press "
".
For organization administrators, projects are displayed in a table. The table displays the name, creator (user), size, creation and last-modified date of all projects within your organization. You may enter each project by clicking on the project name.
Job Page¶
The Job Page has a search bar at the top and a job table below. The search bar allows you to filter jobs by name, by type, by status, by project, and by creation and last-modified date. The job table displays the name, type, status, project, creation and last-modified date of your jobs. You can perform the following operations to manage your jobs:
- View: Click on a job to view its Job Result and/or submit a feedback.
- Rename: Hover above the job name and you will see a "" icon. Click on it to rename the job.
- Download: Press the "" button to download all the files in the job output in a .zip file.
- Delete: Press the "
" button to delete the job.
File Page¶
The File Page has a search bar at the top and a file table below. The search bar allows you to filter files by name, by size, by project, by source, and by last-modified date. The file table displays the name, size, project, source, and last-modified date of your files. You can perform the following operations to manage your files:
- Rename: Hover above the file name and you will see a "" icon. Click on it to rename the file.
- Download: Press the "" button to download the file.
- Delete: Press the "" button to delete the file.
Sources of a file
The source of a file describes how it is incorporated into the project. Possible values include:
- User Upload: when the file is uploaded/saved by the user,
- PDB / AF-DB: when the file is imported from the corresponding cloud database, or
- The name of a job: when the file is the output of that job.
Account/Profile Page¶
The Account/Profile Page displays your account information, and allows you to manage your account settings. You could change your user name, organization, timezone, email, phone number, and password here. Notably, the timezone setting will affect how the time is displayed for you throughout GeoBiologics.
You can also delete your account here by pressing "Delete My Account". Once you complete the deletion process, we will immediately delete all of your projects, along with all of your job history, files, and notifications. You will no longer be billed.
Account/Billing Page¶
The Account/Billing Page displays your job usage and billing information.
In the "Dashboard" tab, you can see your job usage for each job type in the past week / month or a custom time range.
In the "Billing History" tab, you can view your full billing history, including the billing item, plan name, job and job type, project, cost and balance and bill time.
Admin/Users Page¶
Organization administrators can access the Admin/Users page for managing the users in your organization. This page has a search bar at the top and a user table below. The search bar allows you to filter users by name, by email, by phone number, by size used and by role and activation status. The user table displays the name, activation status (Active or Disabled), email, phone number, organization, role, number of projects, number of jobs, storage used, last login IP and time, and creation date of corresponding users.
You can perform the following operations to manage your users:
- Disable: For users with status "Active" you can disable them to change their status to "Disabled". A disabled user cannot log in to GeoBiologics. If a user leaves your organization, we recommend you disable his/her account. The files of disabled users are accessible to organization administrators.
- Config Role: You can configure the role of a user to be either "Normal User" or "Organization Administrator".
- Detail: Here you can view the detailed usages of the user, including the number of projects created, number of jobs submitted, storage used, and usage for each job type.
- Delete: Click on the text "Del" to delete the corresponding user. This will delete all the projects, jobs, and files of the user, so please be careful.
You can also click the "
" button to add a new user to your organization.
In the popup, please fill in the username, email, phone number and initial password of the new user, and click "Create User" to create the user.
Admin/Organizations Page¶
This is where organization administrators can manage their organization profile and usage.
In the "Organization Detail" page, you can view your organization name, description, activation status, and in the plan table, you can view all of your organization's plans, including the plan name, status, compute, order date, start date and end date.
Click "detail" next to the plan table to enter the "Plan Detail" page, where you can view:
- Plan Info: the plan name, start date and end date.
- Plan Content: Detailed info of what this plan contains, including:
- Compute: the number of cloud computing units available
- Storage quota: the amount of cloud storage space available
- Max # Projects: the maximum number of projects allowed
- Max # Jobs: the maximum number of jobs allowed
- Max # Running Jobs: the maximum number of jobs allowed to run simultaneously
- Max # Users: the maximum number of users allowed
- Plan Usage: the usage of compute and each job in the past week / month or a custom time range.
In the "Organization Detail" page, click the "View" button besides "Billing History" to view your organization's full billing history, including the billing item, plan name, user and organization, job and job type, project, cost and balance and bill time.
Support Page¶
The support "page" is actually a separate website hosting GeoBiologics' documentations and tutorials.
You can easily navigate through the support site using the navigation menu. The menu is shown on the left of your screen if it is wider than 1220px; otherwise, you can open it by pressing the "" icon on the top-left.
For each page, if your screen is wider than 960px, you can see a table of contents sidebar on the right, which allows you to quickly navigate to a specific section.
On the top-right and in the navigation header, you should see three buttons: for switching between light and dark mode, for switching between English and Chinese, and for searching the support site.