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 welcome coffees

Simply put: If we don’t know each other we miss out. We miss out on opportunities for collaboration, inter-personal connection, fun, and a richer community. While this usually happens organically – lab meetings, happy hours, unscheduled interactions – basic practices also help. Whenever a new team member joins PennLINC, it is expected that within the first few months of their time in the lab that every existing team member reach out to them to schedule a “welcome coffee”. This doesn’t have to actually involve coffee, but should allow for at least 30+ min to get to know each other. There are many things we can’t control in the world, but we can create a friendly, welcoming, and collaborative environment here.

PennLINC systems onboarding

Once general section-level onboarding is complete (especially CITI/HIPPA training), several systems are needed to function effectively. These include:

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 (just slack DM him your gmail to do so). 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.

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 hosting “static” datasets – e.g., curated datasets as well as processed derivatives. Lab members need a PMACS accoutn to access these resource datasets.

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.

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