Presentation for Transantlantic Educators Dialogue

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Unitat de Farmacologia i Farmacognòsia - Facultat de Farmàcia
Coding tools in Science and
Technology projects
Prof. Dr. Francisco Pérez García
Department of Technology
Pompeu Fabra High School, Martorell, Barcelona (Spain)
SCIENTIX Ambassador
Datura stramonium
Transatlantic Education Dialogue
Collaboration Corner
27 February 2022

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 CONTENTS
 Coding tools: block-based programming vs text-based
programming, easy deep learning and machine learning
 Three sample Science and Technology projects:
 Air pollution project: measuring and analysing data
 Astronomy project: analysing supernovas and exoplanet
 Herbal drugs project: in silico research against
coronavirus

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Coding tools
>2600 Resources
Scientix.eu
website

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Coding tools
Scratch

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Coding tools
MIT App Inventor

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Coding tools
Simple coding
https://ml5js.org/
https://www.w3schools.com/
https://p5js.org/

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Coding tools
w3schools
https://www.w3schools.com/

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Coding tools
p5.js
https://ml5js.org/
https://editor.p5js.org/ ONLINE EDITOR
https://editor.p5js.org/p5/sketches EXAMPLES

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Coding tools
ml5.js: Easy machine learning
https://ml5js.org/
https://www.w3schools.com/
https://examples.ml5js.org/

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Coding tools
Teachable machine
https://teachablemachine.withgoogle.com/

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Teachable machine example
Teachable machine
https://pompeu.neocities.org/tensorflow

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Analysing pollution
Using R library: openair

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Analysing pollution
Using R library: openair

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Analysing pollution
Using R library: openair

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Analysing pollution
Using R library: openair

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http://pompeu.neocities.org/https://pompeu.neocities.
org/airpollution

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Analysing pollution
Using R library: openair
https://davidcarslaw.github.io/openair/
TUTORIALS, FREE BOOK AND DOCUMENTATION
https://blocs.xtec.cat/tecno/science/environment/openair-r/
http://xtec.cat/~fperez5/medi_ambient.html

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Analysing pollution
Microcontroller, sensors and mobile

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Mobile and pollution sensor
https://youtu.be/WzXjr05mrQg

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing the Universe
Objectives
• One student analyse one constellation including myth or
history
• Creation of an interactive image map of a constellation
using GIMP Image Map option and mapper.js Javascript
library and locating sky objects. Another possibility is to
use skysphere.js library.
• Analysis of quick spectra using js9.si.edu website or
SAOImageDS9 software and imageJ to know the
chemical composition percentages.

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Creating a constellation image map
Tools
LEARNING CODING: www.w3schools.com
Learn the basics of Javascript, CSS, HTML, Python, etc with Try it editor
Image constellation from IAU, e.g. https://www.iau.org/public/images/detail/cas/
Finding astronomical data: http://cdsportal.u-strasbg.fr/
GIMP Image editor http://www.gimp.org
Mapper.js available http://www.netzgesta.de/mapper/
Code at my github: https://github.com/drfperez/draco

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Creating a constellation image map
Tools
Available at http://www.gimp.org

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Creating a constellation image map
Map file contents from GIMP
<img src="[Cassiopeia] (imported)" width="1280" height="1280"
border="0" usemap="#map" />
<map name="map">
<!-- #$-:Image map file created by GIMP Image Map plug-in -->
<!-- #$-:GIMP Image Map plug-in by Maurits Rijk -->
<!-- #$-:Please do not edit lines starting with "#$" -->
<!-- #$VERSION:2.3 -->
<!-- #$AUTHOR:Francisco Pérez García -->
<area shape="circle" coords="914,624,18" alt="Cassiopeia A"
href="https://en.wikipedia.org/wiki/Cassiopeia_A" />
</map>

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Creating a constellation image map
Converting map file into html file
<area target="_blank" class="noborder icolor22C2F1" alt="SN 2013hc"
title="SN 2013hc" href="https://wis-tns.weizmann.ac.il/object/2013hc"
coords="363,296,36" shape="circle">
Source code at github.com/drfperez/draco

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Creating an interactive sky sphere
Results
Source code available at:
http://github.com/drfperez/skysphere
Visible at http://pompeu.neocities.org/skysphere

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Radiation from the sky
Radiation being block by atmosphere

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Chandra space telescope

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
ACIS
Advanced CCD Imaginging Spectrometer (ACIS) in Chandra

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
ACIS intrument
Advanced CCD Imaging Spectrometer (ACIS) is an X-
ray imager. X-ray photons hitting the camera are
detected individually and their position, energy and
arrival time recorded. This allows for high resolution
(~1 arcsec) imaging, moderate resolution
spectroscopy and timing studies.

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Resources
Chandra X-Ray Observatory Education:
https://chandra.harvard.edu/edu/
Prof. Kholena (Duke University) website:
https://webhome.phy.duke.edu/~kolena/astroteach.html
Prof. Matilsky (Rutgers University) MOOC:
https://es.coursera.org/learn/analyze

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Finding data to analyse

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Finding data to analyse

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Finding data to analyse

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Finding data to analyse

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Opening data to analyse

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Energy spectrum from js9.si.edu

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Analysing different areas in js9

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Analysing different areas in js9

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Measuring total area in imageJ

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
X-Ray
From
Cassiopea A

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Elements in Supernovae
https://webhome.phy.duke.edu/~kolena/strongxlines.html
https://webhome.phy.duke.edu/~kolena/snrspectra.html

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Fe XVIII: 0.8 keV
Ne X:1.0 keV
Mg XI: 1.34keV
Si XIII: 1.83keV, 2.16 keV
S XV: 2.41 keV
Ar XVII: 3.08keV
Ca XIX: 3.84 keV
Fe XXV: 6.4-6.8 keV
Si XIII means 13 electrons removed from Silicium atom, moving from upper
level 2 to lower level 1 (1.83keV) and from level 13 to 1 (2.7keV)

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools
O VII: 0.557 keV
Ne IX: 0.922 keV
Ne X:1.0 keV
Mg XI: 1.34keV
Si XIII: 1.83keV
S XV: 2.41 keV
Ne X means Neon ionized 9 times (9 electrons removed), T= 3.200.000 K

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing exoplanets from Kepler
Tools
Our python code is available from bit.do/lightkurve

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing anisotropies from supernova
Tools
IMAGEJ and
SAOImageDS9

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Tools

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Analysing data from Chandra
Results from students
Some of my students’ websites:
https://juliaiglesis.neocities.org
https://bertadelvalle.neocities.org/
https://juliaarcas.neocities.org
https://marinamiras.neocities.org/
https://claudiaortiz.neocities.org/
https://ainhoafernandez.neocities.org/
https://claudiaortiz.neocities.org/
https://luciamelero.neocities.org/
https://lauraapolzan.neocities.org/
Some of my websites:
http://blocs.xtec.cat/tecno General blog
http://xtec.cat/~fperez5/index.html
https://pompeu.neocities.org Work in progress

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Erasmus+ 2019-2022 school project
“Touching the past to reach the future”
Ref: 2019-1-TR01-KA229-074244-1
High Schools from Martorell (Spain), Florence (Italy),
Trabzon (Turkey), Bodrum (Turkey),
Naoussa (Greece) and Prague (Czech Republic)
Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Erasmus+ research on herbal drugs
Objectives and tools
 Create an interactive table containing the therapeutical uses and
 composition of near 200 herbal drugs according to the European
 Medicine Agency and European Pharmacopoiea
 Create some powerpoint presentation and mobile apps using
 MIT App Inventor
 Create quiz, guess the word game, alphabet games,etc.
 Study chemical products from plants used against COVID using
 molecular docking: UCSF Chimera, swissdock and
 deep learning library: DeepPurpose
 Information available at our project website:
 https://phytotherapy.neocities.org

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Research on anti-COVID drugs
Objectives and tools
 To know if some natural products from xuebijing injection are
bound to the main protease of coronavirus SARS-CoV-2 (7SI9)
 To use UCSF ChimeraX to create the chemical structures of the
compounds from reference number (e.g. pubchem CID)
and to fetch the protein 7SI9 from protein data bank server
 Use swissdock.ch/docking to perform the docking and
measure binding energies with UCSF Chimera
 Use bit.do/DeepPurpose to find activity using Deep Learning
 Compare with literature research in a scientific poster

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Research on anti-COVID drugs
Objectives and tools
 To know if some natural products from xuebijing injection are
bound to the main protease of coronavirus SARS-CoV-2 (7SI9)
 To use UCSF ChimeraX to create the chemical structures of the
compounds from reference number (e.g. pubchem CID)
and to fetch the protein 7SI9 from protein data bank server
 Use swissdock.ch/docking to perform the docking and
measure binding energies with UCSF Chimera
 Use bit.do/DeepPurpose to find activity using Deep Learning
 Compare with literature research in a scientific poster

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Find possible antiCOVID compounds
Xuebijing

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Find possible anti-COVID compounds
HPLC Xuebijing

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Molecular docking
Compounds to analyze

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Molecular docking
Compounds to analyze

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Molecular docking COVID-19
Domains
Main
protease
of coronavirus
SARS-CoV-2

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Proteasa

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Protein Data Bank
MAIN PROTEASE OF CORONAVIRUS BOUND TO NIRMATRELVIR DRUG

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock CSV

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock CSV

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock CSV

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock CSV

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock CSV

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock CSV

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Prof. Dr. Francisco Pérez García – Departament de Tecnologia – Institut Pompeu Fabra
Projecte de docking molecular
Swissdock CSV

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Favorites > Command line
 labelopt resinfo %(name)s %(number)s
 rlabel: 41,145
 color hot pink :145
 color red :41
El codi anterior pinta de color vermell la HSE 41
(histidina del centre actiu amb un nitrògen
protonat) i de color vermell la CYS 145 (cisteina
145) i escriu el seu nom
Department of Pharmacology and Experimental Therapeutics - School of Pharmacy

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Dr. Francisco Pérez García - Department de Tecnologia - Institut Pompeu Fabra

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Thank you
Questions to fperez5@xtec.cat
https://blocs.xtec.cat/tecno
https://pompeu.neocities.org
http://xtec.cat/~fperez5