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HTS Bioinf - User information page for GDx-bioinf helpdesk

Sammendrag på norsk

Dette er en oversikt over tjenestene som leveres av GDx-bioinf og hvordan brukere kan benytte hjelpesenteret (helpdesk) ved behov for assistanse med bioinformatikk-relaterte saker.

Kjernetjenesten til GDx-bioinf omfatter vedlikehold av bioinformatikksystemer og levering av data fra sekvenseringsmaskiner til tolkere. Hjelpesenteret håndterer mange ulike problemer, som prosjektleveranser, hasteleveranser, brukerstøtte for ELLA og genepanel-builder, metodeutvikling, med mer.

Hjelpesenteret kan nås via e-post og følger en strukturert arbeidsflyt for å håndtere problemer effektivt. Brukere får jevnlig oppdateringer gjennom hele løsningsprosessen.

Scope

This is an overview of the services provided by GDx-bioinf and how users can interact with the helpdesk for assistance with bioinformatics-related issues.

Responsibility

Responsible: GDx unit leader.

Service description summary

The core service provided includes support and maintenance of all operational bioinformatics systems in the department to ensure smooth delivery of data for ordered analyses “from sequencer to interpreter". This encompasses various tasks, a detailed overview of which can be found in the Service level agreement.

Additionally, the service includes collaborative maintenance of the NSC-network according to the Service agreement between "NorSeq" and "AMG-diagnostics".

Types of issues we can help with

The helpdesk handles different types of issues, including:

  • Issues related to delivery of projects with varying priorities, including any missing files or reports
  • NIPT and other deliveries that require urgent attention
  • User support for software maintained by GDx, notably ELLA, anno and Gene panel builder. This includes general questions, handling of errors and performance issues, as well as suggestions for improvements (but see next section).
  • Diagnostic issues related to the NSC-network according to the Service agreement between "NorSeq" and "AMG-diagnostics"
  • Assistance in lab method or procedure development
  • Trend analyses and custom data queries using our diagnostic databases
  • Escalation to TSD (USIT) for stability and performance issues that affect more than one user

    Warning

    For user-specific issues, such as password change, USIT needs to be contacted directly by the respective user

See the Service level agreement for a more detailed overview of the services provided.

Contact us

Users can contact the helpdesk at bioinf-help@medisin.uio.no for requests for support in case of unwanted incidents, general inquiries or routine delivery requests.

To ensure the efficient handling of requests for new feature development, or enhancements that are anticipated to demand substantial resources from GDx-bioinf, a more organized approach is necessary:

  1. To initiate such a request, send an inquiry to the helpdesk first (you will use the helpdesk ticket number for quick communication with GDx-bioinf about the status of your request).
  2. As a next step, helpdesk may ask users to submit a form described in the Teams channel GDx bioinformatikk - informasjon og kontaktskjema (remember to include the helpdesk ticket number).

Follow the procedure HTS Bioinf - Forespørsel til GDx om feilrettinger og utvikling av nye funksjoner in eHåndbok for further guidance on these requests.

Helpdesk Workflow

The helpdesk follows a structured workflow to address user submitted issues efficiently: New issues are defined as "tickets" that are reviewed daily by a helpdesk reviewer (a production responsible bioinformatician), which organizes them by priority and type labels. The reviewer aims to resolve as many tickets as possible on their own. The assigned priority determines the next steps:

  • Urgent and high-priority issues are discussed with the team or the coordinators whenever necessary.
  • Normal priority issues are reviewed weekly. The helpdesk reviewer also goes through and discusses tickets that are in progress, escalates issues when needed, and ensures timely resolution.
  • The issues that have an associated form filled in via the Teams channel GDx bioinformatikk - informasjon og kontaktskjema, are evaluated in the weekly GDx-bioinf coordination meetings.

User guide

  • All inquiries to GDx-bioinf must be routed through the helpdesk by sending an email to bioinf-help@medisin.uio.no. This will create a helpdesk ticket, keeping track of progress and further communication.
  • To ensure the smooth delivery of sequencing projects, all users should provide relevant details to the helpdesk once the project has been set on a sequencer, using the template.
  • Requests should be clearly described in sufficient detail to ensure the helpdesk can understand and address them efficiently.
  • The helpdesk will prioritise urgent tickets. If the helpdesk cannot immediately resolve a ticket, it will be escalated to an appropriately assembled task force.
  • Users can expect regular updates on the status of their tickets until they are resolved. To add more information or request an update on the ongoing ticket, send a reply to the email thread that started when the ticket was first created.
  • If you experience any issues with TSD, ELLA or other GDx operational systems, check the Teams channel GDx bioinformatikk - informasjon og kontaktskjema for any updates, before sending a ticket to helpdesk. GDx takes responsibility for escalating to TSD (USIT) and updating the status in the channel.

Project delivery template

Please send in the project delivery email to bioinf-help@medisin.uio.no once the project is sat on a sequencer. The lines marked with * is the minimal required information to be filled in.

Project delivery: [project_id]

Project [project_id] is now sequencing with the following details:
- sequencing date: YYYY-MM-DD *
- number of samples (blank/control/test samples): *
- Taqman results are available on boston: [Yes/No]
- Number of priority 2/3 samples (wgs only):
- Any hybrid trios:
- Any samples that need to be held before being sent to ELLA (in addition to control and test samples):
- Any additional information needed from the pipeline run, e.g. sensitivity/PPV. If yes, email addresses or TSD location to store the data:
- Any other information relevant for this project delivery: