UROP@CECS workshop: Future Scientist Trends

Daniel Himmelstein (@dhimmel)

2022-12-09 11:00

Vin University, Hanoi, Vietnam

College of Engineering and Computer Science

TBL - C305, Building C

slides.com/dhimmel/vinuni

slides released under CC BY 4.0

How to Become a Modern Open Scientist

event information (tweet)

Event ifno:

Within the scope of Undergraduate Research Opportunities Program (UROP), we are pleased to invite you to UROP@CECS workshop Future Scientist Trends.

Date & time: Friday, 9 December 2022 | 11:00am – 12:50pm
Venue:  TBL - C305, Building C, VinUni campus

College of Engineering and Computer Science

Abstract:

During his PhD studies at University of California, San Francisco, Daniel saw opportunities to increase scientific progress by adopting open and collaborative practices. He began efforts to reduce delays at scholarly journals, ensure publications are public & reusable rather than behind paywalls, and to make the process of science open to benefit from real-time global collaboration. Daniel will discuss how open science helped his career and how students at VinUniversity can apply similar techniques such that they will graduate with a public record of scientific contribution appreciated around the world!

Bio:
Daniel is Head of Data Integration at Related Sciences.

when enjoying nature…

when doing science…

https://github.com/Rezmason/matrix

2011, began PhD

& made my code public on GitHub

GitHub contribution heatmap for @dhimmel

https://manubot.org/catalog/

online discussion contributions
(see thinklab.com/p/rephetio/leaderboard)

Visualizing Hetionet v1.0

• Hetnet of biology for drug repurposing
   
• ~50 thousand nodes
  11 types (labels)
   
• ~2.25 million relationships
  24 types
   
• integrates 29 public resources
  knowledge from millions of studies

Hetionet v1.0

Sci-Hub versus Penn Libraries

• Penn Libraries spent $13.13 million on electronic resources in 2017
• Average per-download cost of $1.61
• 326 toll access articles (manually checked)
  • Penn's access: 80.7%
  • Sci-Hub's database: 94.2%

https://github.com/greenelab/library-access

Publishing Delays

Illustration by Matt Murphy.

© Nature News doi.org/f3mn4t

https://blog.dhimmel.com/history-of-delays/

https://blog.dhimmel.com/plos-and-publishing-delays

files & directories

ISO 8601

how to name files?

01.download-data.ipynb
02.process-data.ipynb
03.visualize-data.ipynb

• Hetionet (≤ v1.0) integrated data from 31 resources:
  • 5 United States Government works
  • 12 openly licensed
  • 4 non-commercial use only
  • 9 were all rights reserved
  • 1 explicitly & contractually forbid reuse
• Requested permission for 11 resources:
  • median time to first response was 16 days
  • 2 affirmative responses
• Other considerations:
  • who owns data
  • incompatibilities: share alike vs non-commercial
  • copyright status of data & fair use
• Solution: license attribute per node/relationship

Legal barriers to data reuse

Recommendations:

1. release data under an open license
2. University researchers: commit to open in your resource sharing plan