ATiM User Guide
From CTRNet Wiki
Contents |
ATiM Overview
ATiM is a web-based application designed and developed by CTRNet in conjunction with leading Canadian biobanks specifically for the operation of biobanks. ATiM is released free for non-commercial use under a General Public License.
Features
- Standard operating procedure integration
- Multi-lingual (French, English)
- Provisions for customization
- Easy addition of additional fields
- User management and system security
- Web-based technology
Modules & Tools
To learn more about the features that the ATiM software provides, please read ATiM (modules & tools presentation).
HOW TO Guides
General Information
Administration
- Where do I find what version of ATiM am I using?
- How to create a new group, which includes setting up access permissions
- How to edit an existing group, which includes editing access permissions
- How to create a new user, which includes setting up their profile, password, and preferences.
- How to edit an existing user, which include editing their profile, password, and preferences.
- Where do I find access logs for existing users?
Customize
These series of guides are targeted to ATiM users that may not have Administrative control, but want to customize how the application works for them. This includes changing their password and customizing their preferences.
- How to update your user profile
- How to change your login password
- How to change your ATiM user preferences
Clinical Annotation
This module was designed to capture all clinical information related to a participant. Consent management is also handled in the clinical module.
- Create a new participant
- Annotate a participant with clinical information
- Assign a protocol to a treatment
- Copy protocol information to a treatment record
- Link my participant to an existing collection
- View a history of clinical events for a participant
- Use the diagnosis section
Inventory
- Create collected specimens and aliquots
- Create tissue, tissue tube and tissue block (See previous guide)
- Create blood and blood tube (See previous guide)
- Create urine and urine tube (See previous guide)
- Create sample aliquots (Ex: tube, block, slide, etc) (See previous guide)
- Define/Change aliquot position into a storage
- Create derivatives and aliquots
- Create DNA extraction from tissue block (See previous guide)
- Create RNA extraction from PBMC tube (See previous guide)
- Create Plasma from Blood tube (See previous guide)
- Create/Define realiquoted aliquots
- Create DNA tubes from a parent DNA tube (See previous guide)
- Create tissue slide from tissue block (See previous guide)
- Create a tissue core from a tissue block (See previous guide)
- Create a whatman paper from a blood tube (See previous guide)
- Define an aliquot as reserved for study
- Create an aliquot internal use
- Create a DNA quality control
- Annotate specimen creating path review
- Annotate tissue (See previous guide)
- Annotate blood (See previous guide)
- Create tissue path review (See previous guide)
Storage
- Create a freezer including shelves and racks
- Create a fridge including shelves and racks (See previous guide)
- Create a nitrogen container including racks (See previous guide)
- Create a box and set box into a freezer
- Create any type of storage and set it into a parent storage (Ex: box on a shelf, rack on a shelf, shelf into a fridge, etc) (See previous guide)
- Move a box from a rack to another rack
- Move any type of storage from one parent storage to another (Ex: move rack from one shelf to another one, etc) (See previous guide)
Query and Report Centre
- Run an existing report
- Export results from a query or batch set
- What are Saved Queries and My Favorites for
- Browse data using the Databrowser
