INTRODUCTION

"Following our first biomedicine research event in June 2017, SVAI is excited to announce our second gathering focused on papillary renal-cell carcinoma type 1

In partnership with RareKidneyCancer.orgSVAI will bring together 150 computer scientists and biomedicine researchers in San Francisco for an intense weekend of computational biomedicine exploration. Interdisciplinary teams will work to further understand and develop treatment options and standard of care for p1RCC. This event will focus on analyzing genomic data with advanced computational methods to look for drug treatment pathways and other potential interventions.

Papillary renal-cell carcinoma, accounts for between 15 to 20% of all kidney cancers. It occurs in the cells lining the small tubules in the kidney that filter waste from the blood and make urine. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist."

 Follow the projects at research.sv.ai.

 

MORE ON COLLABORATIVE RESEARCH EVENTS (aka “Hackathons”)

SVAI uses “collaborative research events” (CREs) to apply the power of the computational biology community to the needs of targeted patient communities.  Like a movie production company, CREs pool the talents of a diverse set of participants for a short period of time to create a well defined deliverable.  CRE deliverables increase knowledge about the disease of interest and can be leveraged in future CREs.  For example the July 2017 CRE lasted 3 days and centered on NF2.  During that time, two groups made especially significant progress.

  • The “AutoNF2 Team” extracted interaction networks from complex genomic data using “deep learning” by feeding an Autoencoder a vector of gene expressions (FPKM) to doing dimensionality reduction.  Large network weights indicated which feature was important.  Using this approach, the team postulated “miR-200a as a potential circulating marker for NF2”
  • The “C3 Team” created 7 mutational signature clusters of brain cancer using 290 glioblastomas and 286 gliomas from TCGA.  Cluster analysis suggested that drugs targeting homologous repair, e.g. PARP inhibitors, could be used to treat the NF2 patient.

The p1RCC CRE will apply these NF2 CRE methods to the p1RCC dataset.

 

PURPOSE

  • Contribute to a real, ongoing patient case.
  • Advance research for rare kidney cancer.
  • Create intersectionality between computer scientists and biologists.
  • Develop new skills in computational biology and cancer genomics.
  • Continue building an open community for collaborative biomedicine research.

 

PROBLEM TRACKS

  • Create a pRCC clonal evolution model using sequencing info from individual pRCC cases.  Here's an similar model for chRCC.
  • More TBD

 

DATASET

TCGA has authorized us to use their full Dataset.  They have two requirements.  First, we must list all event participants as collaborators in the project description we send to them.  So please let us know about your intent to participate as soon as possible.  Second, the participants must agree not to take the controlled access data home and further distribute it.

In addition, James Hsieh from the RCC Trial Consortium has pledged seven targeted exomes for the event.

Finally, SVAI is in discussion with several Sequencing companies to provide new personalized genomes of existing p1RCC patients.

 

WHY YOU SHOULD COME

  • Advanced learning in computational biology and cancer genomics.
  • Great mentoring sessions.
  • Make new friends.
  • Connect with us and our event partners.
  • Our first research event was amazing, and this one will be even better.

 

Space is limited. We will be inviting 150 people to participate in this event in-person.

Rules and Genomic Data Usage Agreement

 
 

AGENDA

Here's the full schedule for the weekend [PDF].

 

EVENT COMMUNICATIONS

We created a few slack channels for easy communication during the event Join: #SolveRKC or #RKC-remote. 

Join Our Slack Channel



COMPUTATIONAL POWER

Coming Soon - TBD.

 

MENTORING SESSIONS

Our mentors will float around during the event and check in with teams to help with problems and answer questions. Please feel free to seek them out at the event and say hi! Some of our mentors will also be participating on teams, so we may post specific hours they are available to help. Also: Don't hesitate to ask others at the event for help - everyone participating in this event has extraordinary skill.

 

TWITTER

The official event hashtag is: #SolvePRCC.

We will use Twitter for live announcements and updates from the event. Follow us at @SVAIresearch.

 

FACEBOOK

Join our FaceBook Group and share some photos of the event (In-person and remote). Our plan is to periodically live streaming short interviews and broadcasting what people are working on through Facebook. SVAI Facebook.

 

YOUTUBE:

The opening and closing talks will be live streamed on SVAI's Youtube account.

  • Opening Talks: 
  • Closing Talks and Final Presentations:

 

SUBMISSIONS

We'd like to see submissions follow the same format as an (abbreviated) academic poster. Submissions are not restricted to this format and we encourage you to be as creative as you want. Push to Github.

  1. Introduction
  2. Purpose
  3. Approach
  4. Methods / Algorithms / Models
  5. Results and Discussion 

 

FINAL PRESENTATRIONS

Each team or individual will have 5 Minutes to present what they worked on. Presentations will be fast! But don't worry, we will link submissions here afterwards so you can get a closer look at what everyone worked on.

 

JUDGING CRITERIA

Each presentation will be judged on the following criteria weighted in this order:

  1. How well does the solution lead to positive outcomes for Rare Kidney Cancer patient treatment?
  2. How novel is the approach to finding a solution?
  3. Quality and depth of the problem analysis.
  4. Team dynamics, diversity, and intersectionality including cross discipline and specialization collaboration.

 

PRIZES

TBD.

 

OTHER RESOURCES


MASTERS OF CEREMONY


JUDGES


SPEAKERS

Bill_Paseman.jpg

Bill Paseman

Founder, RareKidneyCancer.org

Bill Paseman has been in Silicon Valley since 1980. He was the Founder and Chairman of Calico Commerce from 1994-2000 and currently focuses on Angel Investing through Paseman & Associates, and advancing rare kidney cancer research and patient advocacy  through RareKidneyCancer.org.

Twitter   LinkedIn   Personal Site

Onno Faber

Entrepreneur, NF2 Patient

Founder, NF2 Project

Onno is the Founder of NF2 Project. He previously founded several other startup companies (such as Tapstack), and now focuses full time on NF2 Project, a patient organization research and treatment options for Neurofibromatosis type 2. He will talk about his experience from the first SVAI research event. Onno has engaged in a life long pursuit of creating things and solving problems. He studied architecture, receiving his degree in 2006 ( honors).

 Twitter   LinkedIn

Pete Kane

Director, SVAI, Founder, Healthcare.mn

Peter has done a lot of work building healthcare and technology communities in Minnesota and the SF Bay Area. His academic background is Chinese Language and Literature.

LinkedIn

Bharath Ramsundar 175.png

Bharath Ramsundar

Stanford, UC Berkeley, DeepChem Author

MENTOR / JUDGE

Bharath Ramsundar received a BA and BS from UC Berkeley in EECS and Mathematics and was valedictorian of his graduating class in mathematics. He is currently a PhD student in computer science at Stanford University with the Pande group. His research focuses on the application of deep-learning to drug-discovery. In particular, Bharath is the creator and lead-developer of DeepChem, an open source package that aims to democratize the use of deep-learning in drug-discovery and quantum chemistry. He is supported by a Hertz Fellowship, the most selective graduate fellowship in the sciences.

Twitter   LinkedIn


MENTORS


 

FORMAT

Weekend Hackathon

(Not an overnight event)

 

AGENDA

Friday Night March 2nd

18.00: Doors Open

18.30: Welcome!

19.00: 

20.45: Objectives & Team Formation

23.00: Doors Close

Saturday March 3rd

9.00: Doors Open, Breakfast

10.00: Work

11.00: 

12.00: Lunch

13.30:

15.00: Work

17.30: Dinner

23.00: Doors Close

Sunday March 4th

9.00: Doors Open, Breakfast

10.00: Work

12.00: Lunch

13.00: Work

15.30: Final Submissions

16.00: Presentations & Judging

18.00: Happy Hour, Celebrate!

 

 

TECHNICAL LEVEL:

This is a  technically intensive event, both from a computer science and bio / genomics perspective. Our target audience is Computer Scientists, AI/ML Researchers, Computational Biologists, Genomic Researchers. Students in any of these areas are especially encouraged to apply!

 

VENUE

 

TRANSPORTATION

 

FOOD & DRINKS

 


Reach out to learn more about all sponsorship opportunities at hello@sv.ai


 

FAQ

Why are you doing this?

We think it's a good idea to bring together the smartest people in AI / ML, Biology and Genomics to hack on difficult medical problems.

Is this an overnight Hackathon?

Nope. We believe in healthy sleep.

Do I need to provide my own computational power?

No. Google has you covered. We will be issuing Google Cloud credits at the event.

Who is the target Audience?

Computer scientists, AI researchers, Computational Biologists and eager learners around the world.

Can I participate remotely?

Absolutely! Join here.

Will there be opportunities to continue collaborating on this project after the hackathon?

Yes.

 

 


 

Standard Event Disclosures

We have a pretty thorough FAQ, please check it out here: FAQ

CODE OF CONDUCT:

Our conference is dedicated to providing a harassment-free conference experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion (or lack thereof), or technology choices. We do not tolerate harassment of conference participants in any form. Sexual language and imagery is not appropriate for any conference venue, including talks, workshops, parties, Twitter and other online media. Conference participants violating these rules may be sanctioned or expelled from the conference without a refund at the discretion of the conference organizers. For full version, please see: confcodeofconduct.com.

PHOTOGRAPHY:

We take photos at our events. Some of these photos will be used on our website. We seek to respect your privacy and ask that if you do not want your photo to appear on SVAI to please email us.

COMMUNICATIONS:

By signing up for this event, you will automatically be added to future SVAI announcements.

PROMOTIONS:

We do not make announcements for non-SVAI events or conferences at our gatherings. Distribution of flyers, printed media or other non SVAI related materials is not allowed at our events. 

IMPORTANT: 

This gathering is limited to 150 people. You MUST be pre-registered to attend. Registration must include your First and Last name, and some of our venues require ID for entry. You do not need to print a paper ticket. We will be checking people in the building lobby. Questions or comments? Tweet to us @SVAIresearch.

 
 

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