The CODATA-RDA Research Data Science Advanced Workshops on Bio-informatics, Climate Data Sciences, Extreme sources of data and Internet of Things (IoT)/Big-Data Analytics

Description

The applied workshops are preceded by a related Summer school (6-17 August 2017) that builds competence in data analysis and security for participants from all disciplines and/or backgrounds from Sciences to Humanities. The four applied workshops run in parallel from 20-24 August 2017.

Summer school: Principles and practice of research data management, curation and security for Open Science using a range of search compute infrastructure, large-scale data handling, analysis, visualization and modeling technique.
Workshop on Extreme sources of data: Introduction to ATLAS Open Data Platforms/Tools, tutorials and CERN LHC.
Workshop on Bioinformatics: computational methods for the management and analysis of genomic and sequencing data.
Workshop on IoT/Big Data Analytics: Big Data tools and technology; real time event processing; low latency query; analyzing social media and customer sentiment.
Workshop on Climate Data Science: Cloud computing platform/tools for Climate Data Sciences including integration and visualization of on-line and local datasets.

Material

Final List of Participants General Information Poster group photo

The CODATA-RDA Research Data Science Advanced Workshops on Bio-informatics, Climate Data Sciences, Extreme sources of data and Internet of Things (IoT)/Big-Data Analytics | (smr 3257)

Go to day

Monday, 20 August 2018

08:30 - 10:45 Registration, Administrative and Financial formalities

Shuttle service from the Adriatico entrance to the Enrico Fermi Building: all financially supported participants lodging at ICTP Guesthouse should reach the Operations and Travel Unit at the Enrico Fermi Building in order to fulfill all financial procedures.
Please bring with you passport and travel receipts.

Registration at Adriatico lower level: only for participants lodging outside ICTP premises.

Location:

Adriatico Guesthouse - Lower Level

10:45 - 11:30 Welcome plenary by CODATA-RDA & other sponsors and coffee break

11:30 - 18:00 IoT/Big Data Analytics

Location:

Adriatico Guest House - Informatics Laboratory

11:30 Introduction to Big Data & IoT Analytics Problem Scope. Analysis of Large Scale Real-Time and Streaming Data/Introduction to Kafka 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

12:30 Lunch break 1h30'

14:00 Lab – Install & Verify Docker Environment for Kafka 1h50'

Speaker:	Okorafor Ekpe (Big Data Academy)
Material:	Slides

15:50 Group photo & Coffee break 25'

16:15 Lab – Creating Topics & Passing Messages. Group Discussion on Problem 1h45'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

11:30 - 18:00 Climate Data Science

Location: Adriatico Guest House - Lundqvist Lecture Hall
- 11:30 An overview of big data issues in the climate sciences 1h0'
  
  Speaker: Adrian Tompkins (ICTP)
- 12:30 Lunch break 1h30'
- 14:00 Analysis, observational systems and forecasts: data sources and approaches 1h50'
  
  Speaker: Adrian Tompkins (ICTP)
- 15:50 Group photo & Coffee break 25'
- 16:15 Trends in data technology: opportunities and challenges for Earth system simulation and analysis 1h45'
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  Speaker: Venkatramani Balaji (Princeton University)

11:30 - 18:00 Bio-informatics

Location:

Adriatico Guest House - Denardo Lecture Hall

11:30 Experiments: Design and Analysis 1h0'

Speakers:	Fotis Psomopoulos (INAB/CERTH), Maria Tsagiopoulou (CERTH)
Material:	Mentimeter responses Slides

12:30 Lunch break 1h30'
14:00 Components of an Experiment. Wh at is a good experiment design? 1h0'

Speakers: Fotis Psomopoulos (INAB/CERTH), Maria Tsagiopoulou (CERTH)
15:00 Data Distributions and Multipl e Hypotheses Adjustment Methods 50'

Speakers: Fotis Psomopoulos (INAB/CERTH), Maria Tsagiopoulou (CERTH)
15:50 Group Photo & Coffee break 25'
16:15 Introduction to basic NGS pipelines 1h45'

Speakers: Fotis Psomopoulos (INAB/CERTH), Maria Tsagiopoulou (CERTH)

Tuesday, 21 August 2018

09:00 - 18:00 IoT/Big Data Analytics

Location:

Adriatico Guest House - Informatics Laboratory

09:00 Design of Kafka topics and partitions 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

10:00 Lab - Designing topics and partitions 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

11:00 Coffee break 30'

11:30 Evaluation of the designs and suggested solutions 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

12:30 Lunch break 1h30'

14:00 Lab - Implement Topics and Partitions for case study 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

15:00 Kafka: Scaling, APIs, Administration & Integration 1h0'

Speaker: Ekpe Okorafor (Big Data Academy)
16:00 Coffee break 15'

16:15 Lab - Streaming and IoT Case Study 1h45'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

09:00 - 18:00 Climate Data Science

Location:

Adriatico Guest House - Lundqvist Lecture Hall

09:00 Climate Data Science outlook and trends 1h0'

Speaker:	Graziano Giuliani (ICTP)
Material:	Slides

10:00 Hands-on Lab 1h0'

Speaker:	Graziano Giuliani (ICTP)
Material:	notes

11:00 Coffee break 30'
11:30 Hands-on-Lab 1h0'

Speaker: Graziano Giuliani (ICTP)
12:30 Lunch break 1h30'

14:00 Using Jupyter Notebooks to visualize different datasets (with and without ROOT) 1h0'

Speaker:	Arturo Sanchez (CERN)
Material:	Material for classes

15:00 Introduction to Blockchain technology and applications 1h0'

Speaker: Martin Saint (Carnegie Mellon University)
16:00 Coffee break 15'
16:15 Introduction to Blockchain technology and applications II 1h45'

Speaker: Martin Saint (Carnegie Mellon University)

09:00 - 18:00 Bio-informatics

Location:

Adriatico Guest House - Denardo Lecture Hall

09:00 Introduction to basic NGS pipelines 1h0'

Speaker:	Fotis Psomopoulos (INAB/CERTH)
Material:	Slides

10:00 Short read quality and trimming (part 1) 1h0'

Speaker: Fotis Psomopoulos (INAB/CERTH)
11:00 Coffee break 30'
11:30 Short read quality and trimming (part 2) 1h0'

Speaker: Fotis Psomopoulos (INAB/CERTH)
12:30 Lunch break 1h30'
14:00 Mapping 1h0'

Speaker: Fotis Psomopoulos (INAB/CERTH)
15:00 Variant calling (part 1) 1h0'

Speaker: Fotis Psomopoulos (INAB/CERTH)
16:00 Coffee break 15'
16:15 Variant calling (part 2 ) 1h45'

Speaker: Fotis Psomopoulos (INAB/CERTH)

Wednesday, 22 August 2018

09:00 - 18:00 IoT/Big Data Analytics

Location:

Adriatico Guest House - Informatics Laboratory

09:00 Introduction to Spark / Spark Streaming 1h0'

Speaker: Ekpe Okorafor (Big Data Academy)
10:00 Real-time Data Processing Using Kafka and Spark Streaming 1h0'

Speaker: Ekpe Okorafor (Big Data Academy)
11:00 Coffee break 30'

11:30 Lab – Setting up Spark & Integrating with Kafka 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

12:30 Lunch break 1h30'

14:00 Lab - Real-time Data Processing Using Kafka and Spark Streaming 2h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

16:00 Coffee break 15'
16:15 Lab - Real-time Data Processing Using Kafka and Spark Streaming 1h45'

Speaker: Ekpe Okorafor (Big Data Academy)

09:00 - 18:00 Climate Data Science

Location:

Adriatico Guest House - Lundqvist Lecture Hall

09:00 PKI based Data Colouring for securing and sharing open-data in Cloud Environments 1h0'

Speaker:	Mary-Jane Sule (University of Jos)
Material:	Slides

10:00 LAB Data colouring of images 1h0'

Speaker:	Mary-Jane Sule (University of Jos)
Material:	Hands-on Sample image

11:00 Coffee break 30'

11:30 The European Organization for Nuclear Research (CERN): a bit of physics and methods 1h0'

Speakers:	Arturo Sanchez (CERN), Leonid Serkin (CERN)
Material:	Slides

12:30 Lunch break 1h30'

14:00 The European Organization for Nuclear Research (CERN): a bit of physics and methods 2h0'

Speakers:	Arturo Sanchez (CERN), Leonid Serkin (CERN)
Material:	Material for classes

16:00 Coffee break 15'
16:15 Open discussion/review 1h45'

09:00 - 18:00 Bio-informatics

Location: Adriatico Guest House - Denardo Lecture Hall
- 09:00 Introduction to DM and ML, Machine Learning basic concepts 1h0'
  
  Speakers: Amel Ghouila (Institut Pasteur de Tunis / H3Bionet), Fotis Psomopoulos (INAB/CERTH)
- 10:00 Taxonomy of ML and examples of algorithms 1h0'
  
  Speakers: Amel Ghouila (Institut Pasteur de Tunis / H3Bionet), Fotis Psomopoulos (INAB/CERTH)
- 11:00 Coffee break 30'
- 11:30 Applications of ML in Bioinformatics 1h0'
  
  Speakers: Amel Ghouila (Institut Pasteur de Tunis / H3Bionet), Fotis Psomopoulos (INAB/CERTH)
- 12:30 Lunch break 1h30'
- 14:00 P racticing usin g the built - in R data set iris 1h0'
  
  Speakers: Amel Ghouila (Institut Pasteur de Tunis / H3Bionet), Fotis Psomopoulos (INAB/CERTH)
- 15:00 RNASeq analysis using clustering in R 1h0'
  
  Speakers: Amel Ghouila (Institut Pasteur de Tunis / H3Bionet), Fotis Psomopoulos (INAB/CERTH)
- 16:00 Coffee break 15'
- 16:15 RNASeq analysis in R to be continued 1h45'
  
  Speakers: Amel Ghouila (Institut Pasteur de Tunis / H3Bionet), Fotis Psomopoulos (INAB/CERTH)

Thursday, 23 August 2018

09:00 - 18:00 IoT/Big Data Analytics

Location:

Adriatico Guest House - Informatics Laboratory

09:00 Introduction to NoSQL 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

10:00 Real-time Data Pipeline (Kafka -> Spark Streaming -> Cassandra) 1h0'

Speaker: Ekpe Okorafor (Big Data Academy)
11:00 Coffee break 30'

11:30 Lab – Setting up Kafka - Spark streaming - Cassandra 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

12:30 Lunch break 1h30'
14:00 Lab – Real-time Data Pipeline – writing to Cassandra 2h0'

Speaker: Ekpe Okorafor (Big Data Academy)
16:00 Coffee break 15'
16:15 Lab – Real-time Data Pipeline – writing to Cassandra 1h45'

Speaker: Ekpe Okorafor (Big Data Academy)

09:00 - 18:00 Bio-informatics

Location: Adriatico Guest House - Denardo Lecture Hall
- 09:00 Introduction to ChIP - Seq, ATAC - Seq, BS - Seq 1h0'
  
  Speakers: Gabriele Schweikert (University of Tuebingen), David Helekal (University of Dundee)
- 10:00 Retrieving and Preprocessing ChIP - Seq Data 1h0'
  
  Speakers: Gabriele Schweikert (University of Tuebingen), David Helekal (University of Dundee)
- 11:00 Coffee break 30'
- 11:30 Defining Regions of Interests (part 1) 1h0'
  
  Speakers: Gabriele Schweikert (University of Tuebingen), David Helekal (University of Dundee)
- 12:30 Lunch break 1h30'
- 14:00 Defining Regions of Interests (part 2 ) 1h0'
  
  Speakers: Gabriele Schweikert (University of Tuebingen), David Helekal (University of Dundee)
- 15:00 Differential Shape Analysis (MMDiff2) (part 1) 1h0'
  
  Speakers: Gabriele Schweikert (University of Tuebingen), David Helekal (University of Dundee)
- 16:00 Coffee break 15'
- 16:15 Differential Shape Analysis (MMDiff2) (part 2 ) 1h45'
  
  Speakers: Gabriele Schweikert (University of Tuebingen), David Helekal (University of Dundee)

09:00 - 18:00 Climate Data Science

09:00 Lab - Python APIs for remote data access, and the Copernicus Toolbox 2h0'

Speaker: Adrian Tompkins (ICTP)
11:00 Coffee break 30'

11:30 High-Performance Computing 1h0' ( Adriatico Guest House - Lundqvist Lecture Hall )

Speaker:	Ivan Girotto (ICTP)
Material:	Slides

12:30 Lunch break 1h30'

14:00 Cloud Based Data integration and Visualization without programming 2h0'

Speaker:	Omer Muhammad Ayub (King Abdul Aziz University)
Material:	Slides

16:00 Coffee break 15'
16:15 Review 1h45'

Friday, 24 August 2018

09:00 - 12:30 Climate Data Science

Location: Adriatico Guest House - Lundqvist Lecture Hall
- 09:00 Real-time Sentiment Analysis (including Twitter) with Iot/BDA group 1h0'
- 10:00 CDS project HUB - Guided open discussions /projects 1h0'
- 11:00 Coffee break 30'
- 11:30 Feedback, open discussion & Workshop closing 1h0'
09:00 - 12:30 Bio-informatics

Location: Adriatico Guest House - Denardo Lecture Hall
- 09:00 Introduction to Regression 1h0'
  
  Speakers: Fotis Psomopoulos (INAB/CERTH), Amel Ghouila (Institut Pasteur de Tunis / H3Bionet)
- 10:00 Hands - on application: regression algorithms - pros and cons 1h0'
  
  Speakers: Fotis Psomopoulos (INAB/CERTH), Amel Ghouila (Institut Pasteur de Tunis / H3Bionet)
- 11:00 Coffee break 30'
- 11:30 Closing, Final Remarks, Post - workshop survey 1h0'

09:00 - 12:30 IoT/Big Data Analytics

Location:

Adriatico Guest House - Informatics Laboratory

09:00 Real-time Sentiment Analysis 1h0'

Speaker:	Ekpe Okorafor (Big Data Academy)
Material:	Slides

10:00 Lab – Setting up Real-time Query Stack 1h0'

Speaker: Ekpe Okorafor (Big Data Academy)
11:00 Coffee break 30'
11:30 Lab - Twitter Stream Sentiment Analysis 50'

Speaker: Ekpe Okorafor (Big Data Academy)
12:20 Recap & Course Close 10'