Link

Welcome to PennLINC!

This page is geared for new lab members soon after they arrive. Below is a checklist of tasks required to get access to relevant systems. Beyond this, the information on ths site (especially the pages in this “Lab Basics” section) is a good place to start for information on lab meetings, resources for new members, software and environments, and tutorials.

General section onboarding

PennLINC sits within the Neurodevelopment and Psychosis Section of the Department of Psychiatry. As such, there is are several section-level onboarding steps that are detailed here. Note that this page requires PennKey access; getting a PennKey and other initial tasks are coordinated by Stace Moore (stacem@pennmedicine.upenn.edu) as the primary personnel liaison for the section.

PennLINC onboarding

Once general section-level onboarding is complete (especially CITI/HIPPA training), several systems are needed to function effectively. Tinashe Tapera, our senior data analyst, can provide access to some of these systems, including:

Slack: Our primary means of communication as a team. However, also read the page on communication and collaboration.

Google Calendars: Ted maintains an open/public calendar to facilitate scheudling of project meetings. You will need to be given persmissions to make events on this calendar. There is also a PennLINC calendar that integrates events and talks that we will add you to; it is mirrored on the front page of pennlinc.io.

Github: all code belongs in our github code repository; our github pages webpage associated with this organization also houses growing knowledge base of tutorials.

Trello: a web app for tracking tasks and work as a team.

Flywheel: Our main imaging database and analytics platform.

Website: Our front-facing website. Go to the “team form” under “more” to create your profile so you can appear on the “team” page. Ask Tinashe for this password on Slack.

Additionally, we use two compute platforms that you will need access to.

PMACS: We use the PMACS low performance cluster (LPC) for project-specific analyses. See the PennLINC PMACS page for details on how get access and create a project.

CUBIC: We use the large high performance cluster (HPC) named CUBIC for large volumes of parallelizable subject-specific processing jobs. Additionally, specific projects may use CUBIC due to specific computational or software requirements. See the CUBIC page for more information; it is a large compute resources created by our collaborators in the Center for Biomedical Image Computing and Analytics (CBICA). See the PennLINC CUBIC page for details on how to gain access, create projects, and other tips.


Table of contents