Marine Ecosystem Sustainability IGERT : Interdisciplinary Graduate Education in Alaska
IGERT Drexel Open Notebook Science Talk
-
Upload
jean-claude-bradley -
Category
Education
-
view
631 -
download
0
description
Transcript of IGERT Drexel Open Notebook Science Talk
![Page 1: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/1.jpg)
Open Notebook Science as an efficient means for transparency in science
April 15, 2011
IGERT Drexel Meeting
Jean-Claude Bradley
Department of ChemistryDrexel University
![Page 2: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/2.jpg)
The current state of transparency in scientific communication
Case study of melting point data
![Page 3: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/3.jpg)
The Chemical Information Validation Sheet
567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
![Page 4: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/4.jpg)
The Chemical Information Validation Explorer
(Andrew Lang)
![Page 5: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/5.jpg)
Discovering outliers for melting points (stdev/average)
![Page 6: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/6.jpg)
Investigating the m.p. inconsistencies of EGCG
![Page 7: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/7.jpg)
Investigating the m.p. inconsistencies of cyclohexanone
![Page 8: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/8.jpg)
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting
points
![Page 9: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/9.jpg)
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling
points
![Page 10: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/10.jpg)
Sigma-Aldrich, Acros and Wolfram Alpha apparently
DO NOT use the same sources for flash points
![Page 11: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/11.jpg)
Most popular data sources
![Page 12: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/12.jpg)
Alfa Aesar donates melting points to the public
![Page 13: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/13.jpg)
Open Melting Point Explorer
![Page 14: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/14.jpg)
Outliers
MDPI dataset
EPI (via ChemSpider)
![Page 15: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/15.jpg)
Outliers
Alfa Aesar
![Page 16: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/16.jpg)
Inconsistencies and SMILES problems within MDPI dataset
![Page 17: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/17.jpg)
MDPI Dataset labeled with High Trust Level
![Page 18: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/18.jpg)
Open Melting Point Datasets
![Page 19: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/19.jpg)
Open Random Forest modeling of Open Melting Point data using CDK descriptors
(Andrew Lang)
R2 = 0.78, TPSA and nHdon most important
![Page 20: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/20.jpg)
Melting point prediction service
![Page 21: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/21.jpg)
Using melting point for temperature dependent solubility prediction
![Page 22: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/22.jpg)
Motivation: Faster Science, Better Science
![Page 23: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/23.jpg)
There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data
provenance by making assumptions explicit
![Page 24: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/24.jpg)
TRUST
PROOF
![Page 25: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/25.jpg)
First record then abstract structure
In order to be discoverable use Google friendly formats (simple HTML, no login)
In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets)
Strategy for an Open Notebook:
![Page 26: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/26.jpg)
Crowdsourcing Solubility Data
![Page 27: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/27.jpg)
Data provenance: From Wikipedia to…
![Page 28: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/28.jpg)
…the lab notebook and raw data
![Page 29: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/29.jpg)
Calculations Made Public on Google Spreadsheets
![Page 30: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/30.jpg)
Interactive NMR spectra using JSpecView and JCAMP-DX
![Page 31: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/31.jpg)
Raw Data As Images
Splatter?
Some liquid
![Page 32: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/32.jpg)
YouTube for demonstrating experimental set-up
![Page 33: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/33.jpg)
The importance of raw data availability
Missed in a prior publication on solubility
for this compound
![Page 34: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/34.jpg)
Solubilities collected in a Google Spreadsheet
![Page 35: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/35.jpg)
Rajarshi Guha’s Live Web Query using Google Viz API
![Page 36: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/36.jpg)
Web services for summary data
(Andrew Lang)
![Page 37: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/37.jpg)
Web service calls from within a Google Spreadsheet for solubility measurement and
prediction
(Andrew Lang)
![Page 38: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/38.jpg)
Integration of Multiple Web Services to Recommend Solvents for Reactions
(Andrew Lang)
![Page 39: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/39.jpg)
![Page 40: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/40.jpg)
![Page 41: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/41.jpg)
![Page 42: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/42.jpg)
Reaction Attempts Book
![Page 43: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/43.jpg)
Reaction Attempts Book: Reactants listed Alphabetically
![Page 44: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/44.jpg)
ONS Challenge Solubility Book cited for nanotechnology application
![Page 45: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/45.jpg)
Lulu.com Data Disks
![Page 46: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/46.jpg)
Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and
Bradley)
(Don Pellegrino)
![Page 47: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/47.jpg)
All ONS web services
![Page 48: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/48.jpg)
For all Formats of ONS Projects
![Page 49: IGERT Drexel Open Notebook Science Talk](https://reader036.fdocuments.net/reader036/viewer/2022070303/549aa452b479591f098b4576/html5/thumbnails/49.jpg)
Conclusions
•Our current system of publication is not as transparent as it could be
•Open Notebook Science offers an efficient way to make research transparent and discoverable