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PRACTICAL COURSE

POPULATION GENOMICS: BACKGROUND AND TOOLS

Procida, Italy 30 March - 06 April 2019

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yay yay cnr
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yay#EMBOpopgen

Connections

WiFi and SSH instructions here

Timetable

Speakers schedule

  • Anders Albrechtsen - March 30th, April 5th
  • Chiara Batini - March 30th, April 6th
  • Andrew Clark - March 30th, April 2nd
  • Vincenza Colonna - March 30th, April 6th
  • Mathias Currat - March 31st, April 4th
  • Margherita Francescatto - Marco Chierici - April 1st, April 6th
  • Garret Hellenthal - April 1st, April 5th
  • Andrea Manica - March 30th, April 6th
  • Daniel Robert Schrider - March 31st, April 6th

All raw data and software are available on the INFN machine

Days Lessons Tutorials
day 1 Overview
day 2am BasicPopGenConcepts AlleleFrequencies - InfiniteSite - WrightFisherSimulations - SampleData1 - SampleData2 - SampleData3
day 2pm Coalescent simulatecoalescencetrees - CoalescenceExercises
day 3am Gene Genealogy Methods For Demographic Inferences Coalescent simulations and ABC
day 3pm Coalescent simulations in time and space Coalescent simulations in time and space
day 4am ClusteringAlgorithms ClusteringAlgorithmsPractical
day 4pm HapBasedDemography HapBasedDemographyPractical - Python2
day 5am Simple Relationships Practical1
day 5pm Complex Relationships Practical2
day 6 Natural Selection Practicals on Natural Selection
day 7 Intro to ML - Classical ML Practical_ML_1 - Practical_ML_2
day 8

Pompei - Ercolano

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Pompei and Ercolano are two famous archaeological sites that lie in the shadow of mount Vesuvius, the active volcano that dominates the area.

They were destroyed by pyroclastic flows during the massive eruption of Vesuvius in 79 AD.

Go to the central train station at Piazza Garibaldi. You'll find the Circumvesuviana (the train system that connects the Napoli and the towns and cities in the region around Vesuvius) on the lower level of the station. Buy tickets (about 3 euro each way) and take the Circumvesuviana to Pompei Scavi. Note that other regional trains go to the modern city of Pompei but you will need to walk about 25 minutes from that station to the archaeological site while the station Pompei Scavi is just a few minutes from the entrance to the park. A single cafeteria serves the site, so you may want to bring snacks. It can be hot and there is virtually no shade, so dress accordingly. Pompei is a vast ruin, and a walk through most of it should take at least three hours.

Ercolano lies on the same train line as Pompei, but is closer to Napoli. To get there, leave the Circumvesuviana at Ercolano Scavi, and walk down the hill towards the sea for about ten minutes. Ercolano is much smaller than Pompei, but what it lacks in size it makes up in the quality of its preservation. It is possible to visit both sites in one day, but you will probably want to start early.

Naples - city center

This is a list of places that might be interesting. It is not comprehensive and reflects our personal suggestions :)

Place address map description
OAK Napoli Wine And Craft Beer Vico Quercia, 10, 80134 Napoli NA https://goo.gl/maps/gorjLaBWn6B2 craft beer, very pleasant
Il Birraiuolo - Craft Beer Bar Via Vincenzo Bellini, 48, 80135 Napoli NA https://goo.gl/maps/2aJbcmvdQN12 craft beer
Ecomesarà Via Santa Chiara, 49, 80134 Napoli NA https://goo.gl/maps/vgKinko8qrC2 lunch or dinner, fancy, fusion
Vitto Pitagorico Piazza Museo, 15, 80135 Napoli NA https://goo.gl/maps/C9cRw7hpMmo vegetarian, vegan
Un Sorriso Integrale Amico Bio Vico, Via S. Pietro a Maiella, 6, 80138 Napoli NA https://goo.gl/maps/z1MY9Lz4iZ72 vegetarian, vegan
Gay-Odin Via Benedetto Croce, 61, 80134 Napoli NA https://goo.gl/maps/yN6X4aa68fm chocolate, ice cream
Di Matteo Via dei Tribunali, 94, 80138 Napoli NA https://goo.gl/maps/QEGzfnaQAi12 pizza, one of the best
Palazzo Petrucci Pizzeria Piazza S. Domenico Maggiore, 5/6/7, 80134 Napoli NA https://goo.gl/maps/tEewLhjBXkK2 pizza, great location, amazing pizza, fancy
Perditempo Sas Via S. Pietro a Maiella, 8, 80138 Napoli NA https://goo.gl/maps/maAaCeWbLvw night club
Scagliola / Nicola Via San Pietro A Maiella 15, 80138 Napoli NA https://goo.gl/maps/RwebiQbcgFT2 wine store, great collection of wine and rum
Pizze Fritte da Gennaro " ncopp' e chianche" Via Giuseppe Simonelli, 58, 80134 Napoli NA https://goo.gl/maps/LgQGagbBg322 pizza fritta, unbelivable, you will cry after eating
Mexico Piazza Dante, 86, 80135 Napoli NA https://goo.gl/maps/EHxaGbCqGno caffe, one of the best
Libreria Berisio Via Port'Alba, 28, 80134 Napoli NA https://goo.gl/maps/MhNEYqooytM2 aperitivo, and books, of course
Piazza Bellini 80138 Naples, Metropolitan City of Naples https://goo.gl/maps/KDnxS5zuMWu piazza
Gesù Nuovo Square Piazza del Gesù Nuovo, 2, 80134 Napoli NA https://goo.gl/maps/kw5SWD8d5ex piazza
Mennella Il Gelato Via Toledo, 80134 Napoli NA https://goo.gl/maps/qhxahLqe8U42 ice-cream, one of the best
Piazza S. Domenico Maggiore 80134 Naples, Metropolitan City of Naples https://goo.gl/maps/6yuHboTPZV12 piazza
Naples National Archaeological Museum Piazza Museo, 19, 80135 Napoli NA https://goo.gl/maps/W6vRHYZE9GS2 museum, vast collection of material form Pompei
Napoli Sotterranea Piazza San Gaetano, 68, 80138 Napoli NA https://goo.gl/maps/aZ675pLSVd72 underground city
Purgatorio ad Arco Via dei Tribunali, 39, 80138 Napoli NA https://goo.gl/maps/yBT82B3ET2v underground church, cult of "anime pezzentelle"