Training and Documentation
CSBG (Computational System Biology Group) Science Gateway User Manual
- Create a gateway account in https://sciencegateway.brylinski.org/. Use 'Create account'. Provide your details and you will receive an email for account verification.
- Click the link in the email received and confirm your email. Hint: The email sometimes tend to land on 'Junk email' or 'Trash'.
- When gateway administrator grants access, you would receive a notification email.
- Login to the gateway, You are ready to Search through the SRA!
- When logged in you would be in your home page, User Dashboard.
- Two placeholders, 'Browse Projects' and 'Browse Experiments'
- As a gateway user, you could browse your old projects or experiments using 'Browse Projects' or 'Browse Experiments'.
- To create new projects or experiments navigate through the menu bar on top.
- What is a Project? - Project is a collection of experiments, it groups experiments. When creating an experiment, you can select which project to create with.
- What is an Experiment? - Experiment is the gateway record you create in order to launch a job in a remote cluster/supercomputer/HPC.
Save & Launch an Experiment
- To create a new Experiment from the top menu, navigate to Experiment → Create
- Experiment Name (Mandatory)
- Experiment Description (Optional)
- Project (LOV) - Latest will be the default choice.
- Application (LOV)
- Sharing Settings (Optional) - Share with fellow gateway users.
- Application Inputs (Mandatory)
- Save & Launch
- When providing Application inputs;
- Target structure (Mandatory)
- Provide the rest of the parameters
- Screening library: BindingDB
- Screening library: ChEMBL
- Screening library: DrugBank
- Screening library: KEGG Compound
- Screening library: KEGG Drug
- Screening library: NCI-Open
- Screening library: RCSB PDB
- Screening library: ZINC12
- Auxiliary ligands (Optional Input Files. User can provide none and many as pleased)
- After providing the files you could 'Save' the experiment for later submission. If saved you could edit the experiment prior to launching.
- Once launched, you could cancel the experiment, which will cancel the job running in remote cluster.
Other Gateway Features
- Users can share their experiments with other gateway users. When sharing, can decide on level of access to grant.
- Sharing experiment can be done at any time, at the time of creating, while processing and after the experiment is completed.
- To create new experiments similar to an existing one, you can clone the experiment from ;Experiment Summary' page.
Creating & Browsing Projects
- To create a new Project from the top menu, navigate to Project → Create
- Project Name (Mandatory)
- Project Description (Optional)
- Sharing Settings (Optional)
- To browse existing projects, from top menu, navigate Projects → Browse
- All your previous projects will be listed. To view the experiments within a project, select a project and click 'View'.
- You are now in 'Project Summary' page. You can view all the experiments created under the project. Click on experiment name to view individual experiments.