Spring 2021 Jamboree

A virtual hackathon and kickoff event

The Open Problems for Single-Cell Analysis project is a community effort to standardize benchmarking for single-cell analysis. We aim to hold a remote Jamboree in the Spring of 2021 to bring together and expand the Open Problems Community as we build a resource to drive innovation in single-cell analytics.

hackathon
Published

March 29, 2021

Kickoff presentation

Slides for the Kickoff presentation on March 29 are available on Google Slides. A recording of the talk will be made available here after the session.

Schedule

We have groups joining the jamboree from the Americas and from Europe, so we’ll have a schedule to accomodate multiple time zones. We request that everyone join for the introductory session on Day 1 (3/29/21), but starting on Day 2 (3/30/21) we’ll have an earlier session for folks joining from Europe.

The event will start with a presentation to introduce the Open Problems effort at 8am PT / 4pm GMT+1. We will then break out into coding sessions punctuated by breaks. On Days 2 and 3, we will have group discussions around the infrastructure and long-term plans for Open Problems.

Here’s the full schedule broken down by day:

Day 1

Start (PT) Stop (PT) Start (GMT+1) Stop (GMT+1) Activity
8:00am 9:00am 4:00pm 5:00pm Welcome, introduce the day, answer questions about infrastructure
9:00am 10:30am 5:00pm 6:30pm Divide people into pre-selected teams of 5, work for 90 minutes
10:30am 11:00am 6:30pm 7:00pm Game session: Skribbl.io (in #auditorium on Discord)
11:00am 12:30pm 7:00pm 9:30pm Work for 90 minutes (optional for EU/Afr)
12:30pm 13:00pm 9:30pm 10:00pm Regroup, relax for 30 minutes (optional for EU/Afr)

Day 2

Start (PT) Stop (PT) Start (GMT+1) Stop (GMT+1) Activity
😴 😴 2:00pm 2:15pm Welcome, introduce the day for Europe / Africa
😴 😴 2:15pm 3:45pm Break out into groups
😴 😴 3:45pm 4:00pm Coffee break
8:00am 9:00am 4:00pm 5:00pm Americas come online, start day 2 discussion: “What improvements would make Open Problems more useful for your work?” (in #auditorium on Discord)
9:00am 10:30am 5:00pm 6:30pm Divide people into pre-selected teams of 5, work for 90 minutes
10:30am 11:00am 6:30pm 7:00pm Regroup, relax for 30 minutes
11:00am 12:30pm 7:00pm 9:30pm Work for 90 minutes
12:30pm 13:00pm 9:30pm 10:00pm Regroup, relax for 30 minutes

Day 3

Start (PT) Stop (PT) Start (GMT+2) Stop (GMT+2) Activity
😴 😴 2:00pm 2:15pm Welcome, introduce the day for Europe / Africa
😴 😴 2:15pm 3:45pm Break out into groups
😴 😴 3:45pm 4:00pm Coffee break
8:00am 9:00am 4:00pm 5:00pm Americas come online, wrap up for Europe / Africa (1 slide per person in #auditorium on Discord)
9:00am 10:30am 5:00pm 6:30pm Divide people into pre-selected teams of 5, work for 90 minutes
10:30am 11:00am 6:30pm 7:00pm Wrap up and closing celebration for Americas (1 slide per person in #auditorium on Discord)

Discord

To encourage communication and collaboration during the event, we’re going to use Discord. Discord is a chat and video client that combines the text channels of Slack with video channels that users can freely join and leave to talk and share content. We highly recommend downloading the Discord client for your computer because it’s more reliable than using a browser.

Before the jamboree:

  1. If you don’t already have one, create a Discord account
  2. Download Discord desktop client (required for video calling)
  3. Join our server
  4. Introduce yourself with a 👋in the #introductions channel

Introductory videos

To help orient you to our codebase on GitHub, we’ve created three introductory videos. The first is an overall introduction to the GitHub code, the second is an instructional video on adding a new task, and the third is a walk-through guide to GitHub and AWS SageMaker. We’ve tried onboarding a few different ways and it’s been clear that pre-recorded videos are the best way to get new contributors up and running quickly.

Before the Jamboree:

  1. Watch the Open Problems Repository introduction video
  2. Watch the tutorial on adding a new task
  3. Read the guide for GitHub and AWS SageMaker (video linked in guide)

GitHub and Amazon Web Services (AWS)

To facilitate prototyping during the event, we’re going to use SageMaker Studio notebooks that run Docker images that power the Open Problems benchmarking. These notebooks are the same as Jupyter Lab notebooks, just run on AWS servers. We’ll provide a tutorial video on how to launch SageMaker Studio before the Jamboree.

Before the Jamboree:

  1. If you are unfamiliar with GitHub / Git:
  2. Create a GitHub account
  3. Go through the Hello World tutorial on GitHub:
  4. Read through the CONTRIBUTING.md file that describes the process for adding code to the GitHub repository.

Community Participation Guidelines

We want to make sure this event is inclusive and that all attendees are respected. Here are some guidelines to make sure that we can be as productive and successful as possible.

Be Direct and Kind – We speak directly when we disagree and when we think we need to improve. We are kind in these interactions and communications. We aim to be direct, constructive and positive. One way to achieve being direct and kind is to assume good intent and listen actively before responding. We listen with our head and heart, and assure the head-heart connection before we speak.

Make Space – We value each other’s ideas, styles and viewpoints. We seek diverse perspectives. Diversity of views powers innovation. We are aware of how much time is taken up by dominant members of the group. If we find ourselves dominating a discussion, we recognize the need to step back and encourage other voices to join in. “Winning” is when different perspectives make our work richer and stronger.

Be Inclusive – Community members come from many races, ethnicities, cultures and backgrounds. We are respectful of people with different cultural practices, attitudes, political affiliations and beliefs. We work to eliminate our own biases and prejudices. We think of others’ needs from their point of view. We create an environment where we can bring our whole self to our work – our professional self as well as much of our personal self as we each desire.

Take Responsibility & Stay Curious – We assume best intentions and take responsibility for our impact. We are aware of how intense interactions may affect other people. We do our best to stay curious and ask questions, and are open to the fact that we may not have all the information. If we have harmed someone through our words or actions, we listen carefully, apologize sincerely, and correct the behavior going forward.

Bring Solutions & Lead by Example – Our words and actions matter. By matching our actions with our words, we become examples others want to follow. When frustrations arise, we see it as our responsibility to be part of creating solutions. We design our community and our work for positive behavior and hold others accountable.

Behavior That Will Not Be Tolerated

Personal Attacks – Conflicts will inevitably arise, but frustration should never turn into a personal attack. It is not okay to insult, demean or belittle others. Attacking someone for their opinions, beliefs and ideas is not acceptable. This includes sustained “talking over” or “heckling” of speakers.

Derogatory Language – Hurtful or harmful language, or using vulgar, discriminating, intimidating, threatening or harassing language is not acceptable. Using derogatory language based on someone’s race, color, religion, national origin, age, sex, marital status, ancestry, physical or mental disability, veteran status, gender identity, sexual orientation, or any other protected class will not be tolerated. If you’re unsure if a word is derogatory, don’t use it. See also CZI’s EEO, Harassment & Retaliation Policy.

Sexual Attention or Unwelcome Physical Contact – Sexual attention or unwelcome physical contact is not acceptable. This includes sexualized comments, jokes or imagery in interactions, communications or written materials, as well as inappropriate touching or sexual advances. See also CZI’s EEO, Harassment & Retaliation Policy.

Breach of Confidentiality Obligations – Trust is at the core of our ability to collaborate and to advance our work. Improper access, use, disclosure, or sharing of confidential information will not be tolerated. If unsure, the expectation is that you ask before disclosing or using!

Violence, Threats of Violence – Violence and threats of violence are not acceptable – online or offline. This includes incitement of violence toward any individual, including encouraging a person to commit self-harm.

Intoxication – Drinking alcohol in excess or misuse of prescription drugs (or use of illegal drugs) while working or participating in CZI communities, or pushing others to do so, or making derogatory comments about those who abstain from alcohol or other substances is not acceptable.

Consequences of Unacceptable Behavior

Obviously, we can’t outline every positive or unacceptable behavior or action. Please use good judgement and be professional, even in stressful situations. Inappropriate behavior will not be tolerated and violation can result in you being asked to leave an event or online space, either temporarily or for the duration of the event, or being banned from future events and activities. For non-CZI employees, inappropriate behavior may be reported to your organization. For CZI employees, violation may lead to disciplinary action, up to and including termination of employment.

Reporting

Your notification of any concerns is essential to us. We cannot help resolve a problem unless we know about it. Fiona Griffin from CZI has kindly agreed to be our point of contact for reporting. Therefore, please bring any concerns to Fiona Griffin (fiona.griffin@chanzuckerberg.com) as soon as possible so that we can take whatever steps are necessary to address the situation.

Guidelines inspired by CZI’s Our Values and Approach for Supporting Science