GOBLET AGM 2019

The Global Organisation for Bioinformatics Learning, Education & Training (GOBLET) Annual General Meeting (AGM) will be held in Jakarta, Indonesia at the Universitas YARSI from September 9-11, 2019. The event will be co-located with the International Conference on Bioinformatics (InCoB) 2019, Genomic Medicine Conference (GMC) 2019 and Southeast Asia Pharmacogenomics Research Network (SEAPharm Meeting) 2019. This will be the first joint activity between the GOBLET AGM and InCoB
Registration for the GOBLET AGM will allow free participation in the InCoB Opening Ceremony and joint workshop (see agenda); however, participation in other InCoB 2019 activities will require full-registration (https://incob2019.org/)
GOBLET AGM is open to all working in bioinformatics training who would like to observe the AGM and learn more about GOBLET’s work (limited seats).
 
GOBLET AGM 2019 AGENDA
To download GOBLET AGM 2019 Agenda in PDF format, click here
GOBLET_AGM2019_Agenda_v5
In collaboration with InCoB 2019 local organising committee, GOBLET will host a workshop that will be a joined activity with InCoB 2019 delegates.
Detecting differentially expressed genes with RNA-seq
Instructor: Dr Eija Korpelainen

Bio

Dr Eija Korpelainen works currently as a Product manager at CSC – IT Center for Science. Being the national supercomputing centre, CSC provides bioinformatics services for all the universities and research institutes in Finland. Eija has long experience in enabling life scientists to analyze high-throughput data. She has run over 100 training courses in Finland and abroad, and her team has established a popular YouTube channel with tutorial videos. The book “RNA-seq data analysis – practical approach” by Korpelainen et al has been one of the most popular bioinformatics books in recent years. In order to enable biologists to analyze data more efficiently, her team has developed the open source analysis software Chipster which is used worldwide. Eija has participated in several international consortia including the EU funded EMBRACE, AllBio and SeqAhead, and she is currently the national training coordinator of the European ELIXIR initiative. Eija has been involved in GOBLET from the start.

Eija holds a PhD from the Medical faculty of University of Adelaide, Australia, and she completed her post doctoral research as an EMBO long term fellow in the University of Helsinki, Finland. Eija has over 40 peer-reviewed publications and an H-index of 21.

Workshop details

This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the workshop is thus suitable for everybody.

[The lectures are available as videos, and the participants are requested to view them prior to the workshop. This gives you more time to reflect on the concepts so that you can use the workshop time more efficiently. The lectures are summarized, and questions answered during the workshop].

You will learn how to

-check the quality of reads with FastQC

-infer strandedness with RseQC

-align RNA-seq reads to the reference genome with HISAT2 and STAR

-perform alignment level quality control using RseQC

-quantify expression by counting reads per genes using HTSeq

-check the experiment level quality with PCA plots and heatmaps

-analyze differential expression with DESeq2 and edgeR

-take multiple factors (including batch effects) into account in differential expression analysis

 

Train-the-trainer workshop

This interactive Train-the-Trainer workshop aims to provide individuals new to training, or those wishing to develop their skills,  with guidance and tips for developing and delivering training in bioinformatics, exploring a range of methods appropriate to different learning styles, examining the requirements for a successful course and acquiring appropriate feedback.

The workshop will:

  • provide guidance on general training techniques and appropriate use of methods based on learner needs, including some general do’s and do not’s for successful training
  • provide a framework for successful curriculum design and further development, to enable trainers to build training appropriate to their learner’s needs

By the end of this workshop, trainers should be able to:

  • Recognise the elements of good and bad training
  • Describe the role they play in providing an engaging and comfortable learning environment for their trainees
  • Construct appropriate session / curriculum design for their target audience
  • Explore ideas and inspiration for developing training materials and apply these appropriately
  • Seek and act upon feedback to improve their training through reflective practice

Intended audience

This workshop is suitable for anyone wishing to develop their skills in bioinformatics training.

Biography

Dr Annette McGrath is currently a Principal Research Scientist and Team Leader in life science informatics at CSIRO’s Data61 in Brisbane, Australia where she leads a team working in environmental and conservation genomics. The team focuses on developing new tools and methods to solve the unique data analysis challenges created by high throughput sequencing of either environmental samples or of specimens from Australia’s national biological collections. Additionally, she has a long-standing interest and passion for data science education and training in the life sciences and is a member of GOBLET’s Executive Board.

Annette holds postgraduate degrees in molecular biology (National University of Ireland) and statistics (University of Queensland). Following postdoctoral work on multiple sequence alignment, she has worked in a range of bioinformatics roles across the biotech, not-for-profit and government sectors within Australia and New Zealand. In 2011, she was recruited to CSIRO.

For GOBLET members/affiliates/representative

Please click here to resgister

For Non-GOBLET members/observers

Please click here to register

 

 

Flight Estimates:
  • London, UK to Jakarta, ID: US$850-950
  • Toronto, CA to Jakarta, ID: US$ 900-1,000
  • Brisbane, AUS to Jakarta, ID: US$550 – $650
  • Zurich, CH to Jakarta, ID: US$700 – $800
  • Cape Town, ZA to Jakarta, ID: $750 – $900
Accommodations: 3 nights of accommodation will be covered for the participants by Universitas YARSI and by GOBLET.
Meals: Universitas YARSI will provide coffee break and lunch on AGM days and will sponsor dinner on Monday and Tuesday night (9-10 September 2019), while GOBLET will sponsor dinner on Sunday night (8 September 2019). Breakfasts will be provided by the hotel.
Transit from the Airport to the Hotel and from the Hotel to the conference venue will be arranged for GOBLET representatives. Further details will be made  available upon registration for the event.
GOBLET Gold and Platinum members are eligible for partial reimbursement of travel expenses of up to 500 Euro.
 

Visa Information

Passport/Travel Documents:

Visitors to Indonesia must hold a valid passport or travel document with a minimum validity of six months beyond the intended visiting period.

Visa Exemption/Free Visa

Indonesia provides a visa-free facility to 169 countries under the new visa regulation (see list below). Passport holders of certain countries in the regulation are exempted of having a visa to enter Indonesia. The visa exemption is valid only for 30 days, non-extendable or non-convertible into another kind of stay permit.

Requirements:
  • A valid passport with a minimum validity of 6 (six) months
  • Return Ticket or Through Ticket
Purpose
  1. Leisure, Tourism
  2. Family
  3. Social
  4. Art and Cultural
  5. Goverment visit
  6. Giving lecture/speech or attend a seminar
  7. Attend a meeting held by head office or Representative office in Indonesia
  8. Continue journey to another country
Free Visa Country List

The 169 countries, special administrative regions of a country, and entities are:

Albania
Algeria
Andorra
Angola
Antigua and Barbuda
Argentina
Armenia
Australia
Austria
Azerbaijan
Bahamas
Bahrain
Bangladesh
Barbados
Belarus
Belgium
Belize
Benin
Bhutan
Bolivia
Bosnia and Herzegovina
Botswana
Brazil
Brunei Darussalam
Bulgaria
Burkina Faso
Burundi
Cambodia
Canada
Cape Verde
Chad
Chile
China
Czech Republic
Comoros
Costa Rica
Croatia
Cuba
Cyprus
Denmark
Commonwealth of Dominica
Dominican Republic
East Timor
Ecuador
Egypt
El Salvador
Estonia
Fiji
Finland
France
Gabon
Gambia
Georgia
Germany
Ghana
Greece
Grenada

Guatemala
Guyana
Haiti
Holy See (Vatican City)
Honduras
Hong Kong (SAR of China)
Hungary
Iceland
India
Ireland
Italy
Ivory Coast
Jamaica
Japan
Jordan
Kazakhstan
Kenya
Kiribati
Republic of Korea
Kuwait
Kyrgyzstan
Laos
Latvia
Lebanon
Lesotho
Liechtenstein
Lithuania
Luxembourg
Macao (SAR of China)
Macedonia
Madagascar
Maldives
Malawi
Malaysia
Mali
Malta
Marshall Islands
Mauritania
Mauritius
Mexico
Moldova
Monaco
Mongolia
Morocco
Mozambique
Myanmar
Namibia
Nauru
Nepal
New Zealand
Netherlands
Nicaragua
Norway
Oman
Palau

Palestine
Panama
Papua New Guinea
Paraguay
Peru
Philippines
Poland
Portugal
Puerto Rico
Qatar
Romania
Russia
Rwanda
Saint Kitts and Nevis
Saint Lucia
Saint Vincent and the Grenadines
Samoa
San Marino
Sao Tome and Principe
Saudi Arabia
Senegal
Serbia
Seychelles
Singapore
Slovakia
Slovenia
Solomon Islands
South Africa
Spain
Sri Lanka
Suriname
Swaziland
Sweden
Switzerland
Taiwan (Chinese Taipei)
Tajikistan
Tanzania
Thailand
Togo
Tonga
Trinidad and Tobago
Tunisia
Turkey
Turkmenistan
Tuvalu
Uganda
Ukraine
United Kingdom
United States of America
United Arab Emirates
Uruguay
Uzbekistan
Vanuatu
Venezuela
Vietnam
Zambia
Zimbabwe

If the 30 days of Visit Visa Exemption facility feels insufficient, visitor still can apply for Visa on Arrival (given for 30 days and extendable for another 30 days) or Visit Visa.

Read more about the Visa-free facility here:

 

Where We Are

Accommodations:

Our official partner hotel is the Best Western Plus Kemayoran Hotel (bwpluskemayoran.com/), a 4-star hotel located around 4.6 km from Universitas YARSI (the meeting venue). 3 nights of accommodation will be covered for the participants by Universitas YARSI and by GOBLET. Booking should be made via this link to receive a special price and benefit of hotel transport to the meeting venue.

Transportation To/From Jakarta

Travel By Air

Soekarno Hatta International Airport (CGK)

Soekarno Hatta International Airport is the major international airport serving the greater Jakarta area on the island of Java, Indonesia. Universitas YARSI is situated at around 30 km from CGK. To get to Universitas YARSI or hotel from CGK in the most convenient ways:

  1. Taxi: taxi counters are located on the Arrivals level after customs and outside at the taxi stand.Several Taxi companies operate at Jakarta airport, including Blue Bird, Silver Bird, Golden Bird, and Gamya.
    • Blue Bird taxis are blue and provide basic taxi service from a reliable company.
    • Silver Bird taxis are black and provide premium taxi service at slightly higher rates.
    • Golden Bird is a limousine service.
    • For more information about taxi service, click here.
  2. Online taxi service (fixed rate): marginally cheaper than taxis (meter) for the trip downtown. You can reserve an online taxi by installing these apps in mobile phone prior to departing to Indonesia:

GOBLET Reimbursement Policy

GOBLET Gold and Platinum members are eligible for partial reimbursement of travel expenses of up to 500 Euro.

 

 

Indonesia is known as “The Emerald of The Equator”. It is the largest country in the world to consist entirely of islands (17,508 islands according to the Indonesian Naval Hydro-oceanographic office). If you have few days to spend in Indonesia, we have listed a few popular destinations and trips below to explore the diverse culture, tasty foods and spectacular landscapes of this vibrant country.
Please click here, if you want to register for sightseeing tour package below
1. Old town Jakarta & Jakarta Seaside

Jakarta Old Town tour will take you to explore the history of Jakarta and meet local people of Jakarta. Discover the colonial bank supplies and old currencies at Mandiri Bank Museum and learn the heritage of Betawi culture during the 17th to the 19th century atFatahillah Museum.Enjoy the Jakarta seaside atAncol Beach anddevour fresh and quality seafood at Bandar Djakarta Restaurant.

  • Tour Duration : 12 hours (Full Day)
  • 7 am to 7 pm

Package includes:

  • Standard air conditioned bus
  • Meal box (1x) and Snack (1x)
  • Entrance tickets to Mandiri Bank Museum, Fatahillah Museum, and Ancol
  • Insurance
  • Gas, parking, and retribution
  • Driver, tour leader, and crew.
  • Event banner
  • Souvenir shopping tour.
2. Contemporary Jakarta: Art, Shopping and Landmark

Explore the beauty of modern and contemporary art from Indonesia and around the world at Macan Museum and get the chance to enjoy the combination of Indonesian biodiversity, heritage, and technology at Jakarta Aquarium. At the end of the tour, we will take you to visit Sarinah where you can find premium quality Indonesian product, from ethnic fashion to wooden and rattan furniture.

  • Tour Duration : 12 hours (Full Day)
  • 7 am to 7 pm

Package includes:

  • Standard air conditioned bus
  • Meal box (1x) and Snack (1x)
  • Entrance tickets to Macan Museum and Jakarta Aquarium
  • Insurance
  • Gas, parking, and retribution
  • Driver, tour leader, and crew.
  • Event banner
  • Souvenir shopping tour.
3. Jakarta the shopping paradise

Indonesia is rich of fine art and culture in fashion, jewelry, and culinary. Find the collection of Indonesian product at Alun-Alun Indonesia. You can also shop some premium batik textile and fashion at Batik Keris. Find premium quality Indonesian product, from ethnic fashion to wooden and rattan furniture at Sarinah and discover wide variety of unique merchandise and craft productsby Indonesian Small And Medium-Sized Enterprises at SMESCO.

  • Tour Duration : 12 hours (Full Day)
  • 7 am to 7 pm

Package includes:

  • Standard air conditioned bus
  • Meal box (1x) and Snack (1x)
  • Insurance
  • Gas, parking, and retribution
  • Driver, tour leader, and crew.
  • Event banner
  • Souvenir shopping tour.
4. Jakarta Foodvaganza

Excite the taste buds with Jakarta culinary adventure. Discover Jakarta delights at Pusat Jajananblok S and Sabang Street where you can experience Indonesian cuisine and street food, from satay to fried rice. You can also visit the legendary Ragusa Ice Cream, which has been serving their signature ice cream since 1932.

  • Tour Duration : 12 hours (Full Day)
  • 7 am to 7 pm

Package includes:

  • Standard air conditioned bus
  • Insurance
  • Gas, parking, and retribution
  • Driver, tour leader, and crew.
  • Event banner
  • Souvenir shopping tour.
5. The lush greeneries of Bogor

Feel the Italian atmosphere at the Bogor Little Venice where you can ride gondola and some water activities. Discover the mega biodiversity of Indonesia by visiting Bogor Botanical Garden while enjoying the fresh air and beautiful nature.

  • Tour Duration : 12 hours (Full Day)
  • 7 am to 7 pm

Package includes:

  • Standard air conditioned bus
  • Meal box (1x) and Snack (1x)
  • Entrance tickets to The Little Venice and Bogor Botanical Garden
  • Insurance
  • Gas, parking, and retribution
  • Driver, tour leader, and crew.
  • Event banner
  • Souvenir shopping tour.
6. The highland city of Bandung

Depart from Jakarta, this tour will take you to explore the charm of Sundanese traditional culture and the beauty of nature at Dusun Bambu Leisure Park. You can also feed your adventurous soul by participating in some fun games provided at this ecotourism facility. In the second day, we will visit Dago Dream Park which provides several fun activities and unique photo spots.

  • Tour Duration : 2 days 1 night

Package includes

  • Standard air conditioned bus
  • One night stay at selected accommodation (Bumi Makmur Indah)
  • Meal (3x)
  • Entrance tickets to Dusun Bambu and Dago Dream Park
  • Insurance
  • Gas, parking, and retribution
  • Driver, tour leader, and crew.
  • Event banner
  • Souvenir shopping tour.