Epic programm to develop

1. EPIC 1 school programme
Preliminary activities
Before the start of the School, please:
1. Create a free account on github: https://github.com/
2. Join Discord: https://discord.gg/TTaXfJ6nVU
3. Install conda and test sample notebooks (in notebooks.zip)
(see conda installation instructions in Preliminary_activities.pdf and Discord).
4. Also test these notebooks in GoogleColab.
5. Practice using jupyter notebooks (see tutorials in Preliminary_activities.pdf)
6. Once conda is working in your laptop, install (via conda or pip) the following python
libraries for the python exercises we will work on next week:
jupyter numpy scipy cython mpi4py git vtk
matplotlib h5py imageio pandas scikit-image astropy
yt pythtb (see http://www.physics.rutgers.edu/pythtb/)
Day 1 (18/10/2021)
Session 1: Introduction to GIT (9:00 - 10:00)
Tutor: Luis Manzanillas, Max Planck Institute for Physics, Germany
All participants attend.
https://cern.zoom.us/j/63947776888
• Welcome
• What is GIT?
• How to use?
• What can I do with GIT?
• Usage examples

2. Session 2: Data Analysis with python I (10:00 - 13:00)
Tutora: Lupe Villegas López, Instituto de Óptica IO_CSIC, España
All participants attend.
https://cern.zoom.us/j/63947776888
• Read and write data tables
• Work with data tables
• Basic statistics
• Plots with matplotlib
• Regressions and curve fitting
• Examples
Day 2 (19/10/2021)
Session 3: Data Analysis with python II (9:00 - 13:00)
Tutor: Wladimir Banda-Barragán, Hamburg University, Germany
All participants attend.
https://cern.zoom.us/j/63947776888
• Introduction to VTK, HDF5, and Binary Data Formats
• Reading and handling data from numerical simulations
• Array manipulation, and use of conditionals and loops
• Application to the analysis of 2D simulations of fluid dynamics
• Computation of integrated quantities and clump finding techniques
• Visualisation and interpretation of the results

3. Day 3 (20/10/2021):
Parallel sessions on advanced topics start
Session 4: Image processing (9:00 - 13:00)
Tutor: Andrés Morales Navarrete, Friedrich Miescher Laboratory of the Max
Planck Society, Germany
Participants: Selena Barragán, Kevin Cárdenas, Luis Andrés Chicaiza, Shirley Cuzco,
Daniel Gonzalez, Marlon Stalin Martínez López, Fernando Moncada, Rubén Ortiz, Joseth
Pachacama, Jack Rojas, Valeria Sánchez, and María Subía
https://cern.zoom.us/j/61762718081
• Explanation about bioimages (i.e. fluorescence microscopy)
• Bioimage analysis example: quantifying cell morphology from 2D fluorescence
micrographs
• Importing images and plotting images
• Logical operators (pixel-wise operations)
• Intensity Transformation
• Filters and Fourier transformations
• Segmentation
• Extracting data from segmented images (e.g. cell area, elongation)
Session 5: Astrophysics (session in English, 9:00 - 13:00):
Tutor: Helga Dénes, Astron - the Netherlands Institute for Radio Astronomy,
The Netherlands
Participants: Jennifer Chacón, Jorge Chacón, Angie Carolina Dávila Porras, David
Herrería, Melany Monroy, Elvyn Ojeda, Andy Rubio, and Daniel Villarruel
https://cern.zoom.us/j/64257905671
• Brief explanation on astrophysics behind galaxies and their neutral hydrogen (HI
content).
• Reading in fits data cubes (3D spectral line data - HI data of a galaxy)
• Plotting slices of the 3D data cube and making moment maps

4. • Downloading astronomical images from a database (for the same galaxy as the HI
data)
• Making an overlay of the HI data onto an optical image
• Calculating some basic statistics for the spectra
• Averaging the spectra for the galaxy
• Calculating the HI mass of a galaxy
• Fitting a Gaussian to spectra
Day 4 (21/10/2021):
Session 6: Materials science I (9:00 - 11:00)
Tutor: Leonardo Basile, Escuela Politécnica Nacional, Ecuador
Participants: Selena Barragán, Kevin Cárdenas, Luis Andrés Chicaiza, Daniel Gonzalez,
Marlon Stalin Martínez López, Fernando Moncada, Rubén Ortiz, Joseth Pachacama, Jack
Rojas, Valeria Sánchez, and María Subía
https://cern.zoom.us/j/65287676832
• Introduction to Tight binding models in materials
Session 7: Materials science II (11:00 - 13:00)
Tutora: María José Benítez, Escuela Politécnica Nacional, Ecuador
Participants: Selena Barragán, Kevin Cárdenas, Luis Andrés Chicaiza, Daniel Gonzalez,
Marlon Stalin Martínez López, Fernando Moncada, Rubén Ortiz, Joseth Pachacama, Jack
Rojas, Valeria Sánchez, and María Subía
https://cern.zoom.us/j/65287676832
• Magnetism
• Electron microscopy on magnetic materials
• Magnetic simulations

5. Session 8: Particle physics (9:00 - 13:00)
Tutor: Alejandro Gómez Espinosa, ETH Zurich, Switzerland
Participants: Jennifer Chacón, Jorge Chacón, Shirley Cuzco, Angie Carolina Dávila
Porras, David Herrería, Melany Monroy, Elvyn Ojeda, Andy Rubio, and Daniel Villarruel
https://cern.zoom.us/j/67372386698
• Brief intro to data analysis for high energy physics
• The exercise requires basic knowledge of LHC physics data.
• How to handle it, how to process it and what to look up to.
• This exercise uses real data from one of the LHC experiments.
• Filter the data, make relevant plots and statistically analyze the results.
Day 5 (22/10/2021):
9:00 - 12:00
All participants attend. There will be individual presentations and group presentations.
https://cern.zoom.us/j/63947776888
Student presentations (12 minutes + 3 minutes for questions)
1. Melany Monroy, Data visualization in regards of particle physics
2. Presentation by Team Particles
3. Elvyn Ojeda, Caracterización Comparativa De La Fluencia De Secundarios
Producto Del Flujo De Rayos Cósmicos En El Sector De La Laguna Cóndor Cocha
A 5100 Msnm, Y La Laguna Quilotoa A 3914 Msnm, Para Determinar El Tipo
Adecuado De Detectores De Astropartículas
4. Presentation by Team Astro
Coffee Break (10 minutes)

6. 5. María Subía, Quantitative analysis and simulation of liquid crystal organization
model in human liver tissue
6. Presentation by Team Bio
7. Jack Rojas, Simulation of Elastic Scattering Processes of 1 keV to 10 keV
Electrons in Dielectric Materials
8. Presentation by Team Magnetic
9. Presentation by Team Materials
Individual talk abstracts (talks can be in Spanish or English, speaker’s choice):
• Melany Monroy
Title: Data visualization in regards of particle physics
• Elvyn Ojeda
Title: Caracterización Comparativa De La Fluencia De Secundarios Producto Del
Flujo De Rayos Cósmicos En El Sector De La Laguna Cóndor Cocha A 5100
Msnm, Y La Laguna Quilotoa A 3914 Msnm, Para Determinar El Tipo Adecuado De
Detectores De Astropartículas
• María Subía
Title: Quantitative analysis and simulation of liquid crystal organization model in
human liver tissue
Abstract: This project sought to study the organization of hepatocytes within
human liver tissue. In order to do so, the spatial patterns of apico-basal hepatic cell
polarity were quantified and analyzed through a conceptual an algorithmic
framework. Two physiologically relevant conditions were examined: healthy tissue
and tissue with the pathology of Non-Alcoholic Fatty Liver Disease (NAFLD). After
verifying the presence of a liquid-crystalline order within the tissue, Monte Carlo
simulations of a liquid crystal organization in three-dimensional human liver tissue
were developed, to elucidate the mechanisms underlying tissue organization
(hepatocyte-hepatocyte interactions, boundary conditions, external fields, etc.)
Results showed that liquid-crystalline organizational principles exist in human
tissue.
• Jack Rojas
Title: Simulation of Elastic Scattering Processes of 1 keV to 10 keV Electrons in
Dielectric Materials
More information on:
https://sites.google.com/view/ciencia-latitud-0/EPIC/EPIC-1
https://indico.cern.ch/event/1044499/

7. TEAMS (Final Group Presentations):
GROUP ID Name
Individual
presentations
Parallel Session
Group
presentations
Tutors
TEAM BIO
María Subía TALK #5 4 Image
TALK #6 Andrés
Shirley Cuzco 4 Image
Fernando Moncada 4 Image
Valeria Sánchez 4 Image
TEAM
ASTRO
Jennifer Chacón 5 Astro
TALK #4 Helga
Elvyn Ojeda TALK #3 5 Astro
Andy Rubio 5 Astro
Daniel Villarruel 5 Astro
TEAM
MATERIALS
Luis Chicaiza 6 Materials I
TALK #9 Leonardo
Kevin Cárdenas 6 Materials I
Rubén Ortiz 6 Materials I
Selena Barragán 6 Materials I
TEAM
MAGNETIC
Joseth Pachacama 7 Materials II
TALK #8 María José
Jack Rojas TALK #7 7 Materials II
Daniel Gonzalez 7 Materials II
Marlon Martínez 7 Materials II
TEAM
PARTICLE
Jorge Chacón 8 Particle
TALK #2 Alejandro
Angie Dávila 8 Particle
David Herrería 8 Particle
Melany Monroy TALK #1 8 Particle