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

Administration

Description

During this activity, several applied/thematic workshops on Research Data Science run in parallel.

Bioinformatics: This workshop focuses on building Machine Learning workflows using NGS Data. Topics include: Experimental design; Introduction to NGS data analysis; Machine Learning in NGS; and CWL. Participants should be familiar with UNIX shell and R programming language.
IoT and Big Data Analytics: This workshop presents the analysis of vast amounts of data produced by embedded devices, sensors, appliances and other data-collecting systems in real time using new processes and tools for collecting, storing and processing IoT big data, event/streaming data. Participants should be familiar with software installation and programming in R or Java or Python. Professionals & corporate entities should apply for this workshop via the ITU Academy.
Climate Data Sciences: This workshop will introduce Cloud-Computing based Data access, processing and visualisation tools for Climate Science, including the Copernicus climate data services platforms and the CMIP Earth System Grid. Participants will work in small project teams and should have a background in Climate Sciences and/or climate modeling.
Extreme Sources of Data: This workshop introduces the basics relative to a cut-and-count particle physics analysis as performed in the ATLAS Collaboration (Large Hadron Collider). Topics to be covered include phenomenological, experimental and data-analysis aspects of the Standard Model; software development and tools for analysis and reproducible science and sharing. Participants should have taken at least one course on Particle Physics at High Education level.

Individuals seeking an introduction to Research Data Science can apply to the Summer School that runs immediately before the workshops.

GRANTS:

A limited number of grants are available to support the attendance of selected participants from developing countries.
Professionals and corporate entities should register/apply for the Advanced Workshop on IoT and Big-Data Analytics via the ITU Academy platform.

Material

Fianl 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 3376)

Go to day

Monday, 19 August 2019

08:30 - 08:45

Location: Adriatico Guest House - Kastler Lecture Hall
- 08:30 Opening Ceremony 15'

08:45 - 10:00

Location:

Adriatico Guest House - Lower Level

08:45 Administrative and Financial Formalities 1h15'

REGISTRATION: Upon arrival, Visitors not staying in the ICTP Guest Houses, are kindly requested  to complete registration formalities at the Adriatico Guesthouse as follows: Office 3 -
(Lower level) from 8.45 till 10.00.

TRAVEL UNIT (Only for those Visitors receiving daily living allowance/travel reimbursement, who  have not provided their bank account data through the on-line portal): after having completed    registration formalities, please go to the Travel Unit, Enrico Fermi Building, Main Entrance,    Room T17, ground floor, open two days: Monday and Friday, 08.30 - 12.00  and 13.30 - 14.30.
Please bring with you: badge/identity card or passport, any travel ticket and boarding passes.
A shuttle service from the Adriatico Entrance to the Enrico Fermi Building will be available.

10:00 - 18:00 Climate Data Science Workshop

Location:

Adriatico Guest House - United Nations LH

10:00 Introduction to Python programming – Lab session 1h0'

Speaker:	Elliot MENKAH (Kwame Nkrumah University of Science and Technology)
Material:	Link

11:00 Coffee break 30'
11:30 Introduction to Python Programming – Lab session 1h0'

Speaker: Elliot MENKAH (Kwame Nkrumah University of Science and Technology)
12:30 Lunch Break 1h30'
14:00 Advanced python with anaconda, notebooks and Jupyter 2h0'
16:00 Coffee break 15'

16:15 Presentation of the NetCDF format and tools for visualization/ treatment 1h45'

Speaker:	Charlène GABA (University of Abomey - Calavi, Benin)
Material:	Slides

10:00 - 18:00 Advanced Workshop on Extreme Sources of Data

Location:

Adriatico Guest House - Lundqvist LH

10:00 Introduction to Python programming 1h0'

Speaker:	Elliot MENKAH (Kwame Nkrumah University of Science and Technology)
Material:	Link

11:00 Coffee break 30'
11:30 Introduction to Python programming 1h0'

Speaker: Elliot MENKAH (Kwame Nkrumah University of Science and Technology)
12:30 Lunch Break 1h30'
14:00 Python hands-on session 2h0'
16:00 Coffee break 15'
16:15 Python hands-on session 1h45'

10:00 - 18:00 Advanced Workshop on IoT/Big-Data Analytics
- 10:00 Introduction to Big Data & IoT Analytics Problem Scope. Analysis of Large Scale Real-Time and Streaming Data 1h0'
- 11:00 Coffee break 30'
- 11:30 Introduction to Kafka 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Lab – Install & Verify Docker Environment for Kafka 2h0'
- 16:00 Coffee break 15'
- 16:15 Lab – Creating Topics & Passing Messages. Group Discussion on Problem 1h45'
11:00 - 18:00 Advanced Bioinformatics Workshop

Location: Adriatico Guest House - Informatics Laboratory
- 11:00 Coffee break 30'
- 11:30 Experiments: Design and Analysis 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Components of an Experiment. What is a good experiment design? 1h0'
- 15:00 Data Distributions and Multiple Hypotheses Adjustment Methods 1h0'
- 16:00 Coffee break 15'
- 16:15 Introduction to basic NGS pipelines 1h45'

Tuesday, 20 August 2019

09:00 - 17:00 Advanced Workshop on Extreme Sources of Data

09:00 Introduction to Particle Physics 1h0'

Speaker:	Muhammad ALHROOB (University of Oklahoma)
Material:	Slides

10:00 Discovering particles with the ATLAS Experiment at the LHC 1h0'

Speakers:	Leonid SERKIN (ICTP/Udine/CERN), Muhammad ALHROOB (University of Oklahoma)
Material:	Link Slides

11:00 Group photo 5'
11:05 Coffee break 25'

11:30 Statistical methods and Monte Carlo in HEP 1h0'

Speaker:	Leonid SERKIN (ICTP/Udine/CERN)
Material:	Slides

12:30 Lunch Break 1h30'

14:00 Machine learning at LHC 1h0'

Speaker:	Leonid SERKIN (ICTP/Udine/CERN)
Material:	Slides

15:00 Introduction to the Grid, Cloud and Big Data 1h0'

Speaker:	Arturo SANCHEZ PINEDA (University of Udine)
Material:	Link

16:00 Coffee break 15'

16:15 Introduction to the Grid, Cloud and Big Data 45'

Speaker:	Arturo SANCHEZ PINEDA (University of Udine)
Material:	Link

09:00 - 18:00 Climate Data Science Workshop

Location:

Adriatico Guest House - United Nations LH

09:00 Analysis, observational systems and forecasts: data sources and approaches 2h0'

Speaker:	Adrian TOMPKINS (ICTP)
Material:	Lecture notes Worksheet

11:00 Group photo 5'
11:05 Coffee break 25'
11:30 Lab - Python APIs for remote data access, and the Copernicus Toolbox 1h0'
12:30 Lunch Break 1h30'
14:00 Lab - Python APIs for remote data access, and the Copernicus Toolbox 2h0'
16:00 Coffee break 15'
16:15 Open discussion/review 1h45'

09:00 - 18:00 Advanced Bioinformatics Workshop

Location: Adriatico Guest House - Informatics Laboratory
- 09:00 Introduction to basic NGS pipelines 1h0'
- 10:00 Short read quality and trimming (part 1) 1h0'
- 11:00 Group photo 5'
- 11:05 Coffee break 25'
- 11:30 Short read quality and trimming (part 2) 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Mapping 1h0'
- 15:00 Variant calling (part 1) 1h0'
- 16:00 Coffee break 15'
- 16:15 Variant calling (part 2) 1h45'
09:00 - 18:00 Advanced Workshop on IoT/Big-Data Analytics

Location: Adriatico Guest House - Denardo Lecture Hall
- 09:00 Design of Kafka topics and partitions 1h0'
- 10:00 Lab - Designing topics and partitions 1h0'
- 11:00 Group photo 5'
- 11:05 Coffee break 25'
- 11:30 Evaluation of the designs and suggested solutions 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Lab - Implement Topics and Partitions for case study 1h0'
- 15:00 Kafka: Scaling, APIs, Administration & Integration 1h0'
- 16:00 Coffee break 15'
- 16:15 Lab - Streaming and IoT Case Study 1h45'
18:30 - 20:30

Location: Adriatico Guest House - Terrace
- 18:30 Welcome reception 2h0'
```
All participants are cordially invited to a Welcome Reception.
```

Wednesday, 21 August 2019

09:00 - 18:00 Climate Data Science Workshop

Location:

Adriatico Guest House - United Nations LH

09:00 Analysis, observational systems and forecasts: data sources and approaches 1h0'

Speaker:	Adrian TOMPKINS (ICTP)
Material:	Lecture notes Worksheet

10:00 Lab - Python APIs for remote data access, and the Copernicus Toolbox 1h0'
11:00 Coffee break 30'
11:30 Lab - Python APIs for remote data access, and the Copernicus Toolbox 1h0'
12:30 Lunch Break 1h30'
14:00 Lab - Python APIs for remote data access, and the Copernicus Toolbox 2h0'
16:00 Coffee break 15'
16:15 Open discussion/review 1h45'

09:00 - 18:00 Advanced Workshop on Extreme Sources of Data

Location:

Adriatico Guest House - Lundqvist LH

09:00 Introduction to ATLAS Open Data platform and tools 2h0'

Material:

Class material materials

Google docs instructions

11:00 Coffee break 30'
11:30 Introduction to hands-on session 1h0'
12:30 Lunch Break 1h30'
14:00 ATLAS Open Data Q&A 2h0'
16:00 Coffee break 15'
16:15 ATLAS Open Data Q&A 1h45'

09:00 - 18:00 Advanced Bioinformatics Workshop

Location: Adriatico Guest House - Informatics Laboratory
- 09:00 Introduction to DM and ML, Machine Learning basic concepts 1h0'
- 10:00 Taxonomy of ML and examples of algorithms 1h0'
- 11:00 Coffee break 30'
- 11:30 Applications of ML in Bioinformatics (genomics and metagenomics) 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Practicing using the built-in R data set iris 1h0'
- 15:00 RNASeq analysis using clustering in R 1h0'
- 16:00 Coffee break 15'
- 16:15 RNASeq analysis in R to be continued 1h45'
09:00 - 18:00 Advanced Workshop on IoT/Big-Data Analytics

Location: Adriatico Guest House - Denardo Lecture Hall
- 09:00 Introduction to Spark / Spark Streaming 1h0'
- 10:00 Real-time Data Processing Using Kafka and Spark Streaming 1h0'
- 11:00 Coffee break 30'
- 11:30 Lab – Setting up Spark & Integrating with Kafka 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Lab - Real-time Data Processing Using Kafka and Spark Streaming 2h0'
- 16:00 Coffee break 15'
- 16:15 Lab - Real-time Data Processing Using Kafka and Spark Streaming 1h45'

Thursday, 22 August 2019

09:00 - 18:00 Climate Data Science Workshop

Location:

Adriatico Guest House - United Nations LH

09:00 Use/ usefulness of climate projections for the future; scenarios, 2 degrees : topics to be addressed: uncertainties , trends 2h0'

Speaker:	Charlene GABA (University of Abomey - Calavi, Benin)
Material:	Slides

11:00 Coffee break 30'
11:30 Introduction to HPC and parallel programming 1h0'
12:30 Lunch Break 1h30'
14:00 Overview of Storage infrastructure for Climate Data 2h0'
16:00 Coffee break 15'
16:15 Open discussion/review 1h45'

09:00 - 18:00 Advanced Workshop on Extreme Sources of Data

Location: Adriatico Guest House - Lundqvist LH
- 09:00 Laboratory session: ATLAS Open Data hands-on tutorial 2h0'
- 11:00 Coffee break 30'
- 11:30 Laboratory session: ATLAS Open Data hands-on tutorial 1h0'
- 12:30 Lunch Break 1h30'
- 14:00 Laboratory session review 2h0'
- 16:00 Coffee break 15'
- 16:15 Laboratory session review 1h45'
09:00 - 18:00 Advanced Bioinformatics Workshop

Location: Adriatico Guest House - Informatics Laboratory
- 09:00 Introduction to Nextflow 1h0'
- 10:00 Parameters, Channels and Processes 1h0'
- 11:00 Coffee break 30'
- 11:30 Docker, Executors and Channel Operations 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Practical exercises in Nextflow 1h0'
- 15:00 Practical exercises in Nextflow 1h0'
- 16:00 Coffee break 15'
- 16:15 Practical exercises in Nextflow 1h45'
09:00 - 18:00 Advanced Workshop on IoT/Big-Data Analytics

Location: Adriatico Guest House - Denardo Lecture Hall
- 09:00 Introduction to NoSQL 1h0'
- 10:00 Real-time Data Pipeline (Kafka -> Spark Streaming -> Cassandra) 1h0'
- 11:00 Coffee break 30'
- 11:30 Lab – Setting up Kafka - Spark streaming - Cassandra 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Lab – Real-time Data Pipeline – writing to Cassandra 2h0'
- 16:00 Coffee break 15'
- 16:15 Lab – Real-time Data Pipeline – writing to Cassandra 1h45'

Friday, 23 August 2019

09:00 - 12:30 Climate Data Science Workshop

Location:

Adriatico Guest House - Kastler LH

09:00 Models and Data for Blue Growth strategy: how to become aware of the EU Copernicus Marine Envirnoment Monitoring Services (CMEMS) offer 1h0'

Speaker:	Stefano SALON (OGS, Trieste)
Material:	Lecture notes

10:00 Certificate ceremony 1h0'
11:00 Coffee break 30'
11:30 Feedback, open discussion & Workshop closing 1h0'

09:00 - 12:30 Advanced Bioinformatics Workshop

Location: Adriatico Guest House - Informatics Laboratory
- 09:00 Q & A and bonus examples 2h0'
- 11:00 Coffee break 30'
- 11:30 Closing, Final Remarks, Post-workshop survey 1h0'
09:00 - 12:30 Advanced Workshop on Extreme Sources of Data

Location: Adriatico Guest House - UN Room
- 09:00 Presentations of previous day's work/results by participants 1h30'
- 10:30 Live virtual-visit to ATLAS Control Room 30'
- 11:00 Coffee break 30'
- 11:30 Summary session and hand-out of certificates 1h0'
09:00 - 18:00 Advanced Workshop on IoT/Big-Data Analytics

Location: Adriatico Guest House - Denardo Lecture Hall
- 09:00 Real-time Sentiment Analysis 1h0'
- 10:00 Lab – Setting up Real-time Query Stack 1h0'
- 11:00 Coffee break 30'
- 11:30 Lab - Twitter Stream Sentiment Analysis 1h0'
- 12:30 Lunch break 1h30'
- 14:00 Lab - Twitter Stream Sentiment Analysis 2h0'
- 16:15 Recap & Course Close 1h45'