Difference: EducationMIKSeminars2012 (1 vs. 27)

Revision 27
30 Jan 2012 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  Schedule

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  • 11:30 - 12:30 Lecture: Dutch e-Infrastructure (Tom Visser)
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Revision 26
27 Jan 2012 - Main.BarberaVanSchaik
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  * A bioinformatician’s view (Barbera van Schaik)
* Virus discovery (Lia van der Hoek)
  • 12:30 - 13:15 Lunch.
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Background information
Revision 25
27 Jan 2012 - Main.BarberaVanSchaik
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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* A bioinformatician’s view (Barbera van Schaik)
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* A bioinformatician’s view (Barbera van Schaik)
  * Virus discovery (Lia van der Hoek)
Revision 24
27 Jan 2012 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • 15:00 - 15:15 Recap

Background information
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Seminar 5. e-Bioscience @work 2: DNA Data Analysis on the e-Bioinfra

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* A bioinformatician’s view (Barbera van Schaik)
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* A bioinformatician’s view (Barbera van Schaik)
  * Virus discovery (Lia van der Hoek)

Background information
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  • e-bioinfra website
  • Olabarriaga SD, Glatard T, de Boer PT. A virtual laboratory for medical image analysis. IEEE Trans Inf Technol Biomed. 2010 Jul;14(4):979-85. Epub 2010 Apr 5. (pubmed)
 
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  • see also many links in the slides
 

Seminar 6. Wrap-up and borrel

Contents:
Revision 23
26 Jan 2012 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  Schedule

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  • 11:30 - 12:30 Lecture: Dutch Grid Infrastructure (Tom Visser)
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  • 11:30 - 12:30 Lecture: Dutch e-Infrastructure (Tom Visser)
 
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  Background information
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Seminar 5: e-Bioscience @work 2: DNA Data Analysis

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Seminar 5. e-Bioscience @work 2: DNA Data Analysis on the e-Bioinfra

 
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In this seminar we present how an e-infrastructure can be used for biomedical research to perform DNA data analysis along the lines introduced in previous seminars. Examples of large studies that have been performed at the AMC and in The Netherlands will be presented by a guest speaker. During the practice the students will perform data analysis for a small genomics study using the AMC e-infrastructure for biomedical research, which facilitates access to the Dutch Grid.
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In this seminar we present how an e-infrastructure can be used for biomedical research to perform DNA data analysis along the lines introduced in previous seminars. The available platform (e-bioinfra, AMC e-infrastructure for biomedical research, which is used in the practice for seminar 4) is described in more detail, exposing its main functions. Examples of large studies that have been performed at the AMC and in The Netherlands will be presented by guest speakers. During the practice the students will perform data analysis for a small genomics study using the e-bioinfra.
 

  • 09.30 - 11.30 Lecture: e-Infrastructure for biomedical research (Silvia Olabarriaga)
  • 11:30 - 12:30 Lectures: Analysis of genomics data on the e-bioinfra
    * A bioinformatician’s view (Barbera van Schaik)
    * Virus discovery (Lia van der Hoek)
  • 12:30 - 13:15 Lunch.
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  • 13.15 – 15:15 Practice: [[][virus discovery on the Dutch grid]] (Babera van Schaik)
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Background information
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Tom Visser
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SARA
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SARA, BiGGrid
 

Dr. Lia van der Hoek
Revision 22
25 Jan 2012 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  Presentation
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Computer excercises
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Computer exercises
 

Seminar 3. Bioinformatics@work 2: Variant selection and accounting for data bias

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  Presentation
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Computer excercises
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Computer exercises
 

Seminar 4. e-Bioscience@work 1: e-infrastructures

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In this seminar we will introduce concepts related to e-Bioscience, with focus on "e-infrastructures” that provide resources that enable large scale data analysis for biomedical research. First it will present an overview of state-of-the-art computing technologies used for data-intensive biomedical research, including grids, scientific workflows, and semantic web. It will also provide the opportunity for hands-on experience with the Dutch e-Science infrastructure (BiGGrid).
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In this seminar we will introduce concepts related to e-Bioscience, with focus on "e-infrastructures” that provide resources that enable large scale data analysis for biomedical research. An overview is presented of the state-of-the-art computing technologies used for data-intensive biomedical research, including grids, scientific workflows, and semantic web. An invited lecture presents the developments on the Dutch scenario. This seminar will also provide the opportunity for hands-on experience with the Dutch e-Science infrastructure.
 
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preliminary program
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Schedule

Background information
 

Seminar 5: e-Bioscience @work 2: DNA Data Analysis

In this seminar we present how an e-infrastructure can be used for biomedical research to perform DNA data analysis along the lines introduced in previous seminars. Examples of large studies that have been performed at the AMC and in The Netherlands will be presented by a guest speaker. During the practice the students will perform data analysis for a small genomics study using the AMC e-infrastructure for biomedical research, which facilitates access to the Dutch Grid.
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preliminary program
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  • 09.30 - 11.30 Lecture: e-Infrastructure for biomedical research (Silvia Olabarriaga)
  • 11:30 - 12:30 Lectures: Analysis of genomics data on the e-bioinfra
    * A bioinformatician’s view (Barbera van Schaik)
    * Virus discovery (Lia van der Hoek)
  • 12:30 - 13:15 Lunch.
  • 13.15 – 15:15 Practice: [[][virus discovery on the Dutch grid]] (Babera van Schaik)

Background information
 

Seminar 6. Wrap-up and borrel

Contents:
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  Bioinformatics Laboratory, Academic Medical Centre
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Shayan Shahand
Bioinformatics Laboratory, Academic Medical Centre
  Prof. Dr. Frank Baas
Genomics Facility, Academic Medical Centre
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Tom Visser
SARA

Dr. Lia van der Hoek
Virus Discovery Lab, Academic Medical Centre
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Revision 21
25 Jan 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Presentation
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Computer excercises
Revision 20
25 Jan 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • to be added

Computer excercises
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Seminar 4. e-Bioscience@work 1: e-infrastructures

Revision 19
24 Jan 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  In this seminar you will learn how to prioritize and select variants from exome data. You will also learn how sequencing errors and various biases affect the outcome of an exome sequencing experiment.
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The data analysis will continue where you left of yesterday and you will identify the variant that causes Nicolaides-Baraitser. Analyses will be carried out in a Linux environment with the help of several applications for sequence analysis and the statistical programming language R. All (Linux) commands to successfully perform the analyses will be provided to you, so that you can focus on the interpretation of the results.
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The data analysis will continue where you left of yesterday and you will identify the variant that causes Nicolaides-Baraitser. Analyses will be carried out in a Linux environment with the help of several applications for sequence analysis and the statistical programming language R. Most (Linux) commands to successfully perform the analyses will be provided to you, so that you can focus on the interpretation of the results.
 

Schedule
Revision 18
22 Jan 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Seminar 3. Bioinformatics@work 2: Variant selection and accounting for data bias

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Computer exercises
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Goal
In this seminar you will learn how to prioritize and select variants from exome data. You will also learn how sequencing errors and various biases affect the outcome of an exome sequencing experiment.

The data analysis will continue where you left of yesterday and you will identify the variant that causes Nicolaides-Baraitser. Analyses will be carried out in a Linux environment with the help of several applications for sequence analysis and the statistical programming language R. All (Linux) commands to successfully perform the analyses will be provided to you, so that you can focus on the interpretation of the results.

Schedule
  • 9.30 – 10.30. Lecture. Variant selection and accounting for data bias (Perry Moerland)
  • 10.45 – 13.00. Computer practicum. Identification of the gene mutation causing Nicolaides-Baraitser using exome data: variant selection and bias (Perry Moerland)
  • 13.00 - 13.45. Lunch.
  • 13.45 – 15.00. Computer practicum. Continued. (Perry Moerland)

Background information

Presentation
  • to be added

Computer excercises
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Seminar 4. e-Bioscience@work 1: e-infrastructures

Revision 17
22 Jan 2012 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Revision 16
21 Jan 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  Computer excercises
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Seminar 3. Bioinformatics@work 2: Accounting for data bias

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Seminar 3. Bioinformatics@work 2: Variant selection and accounting for data bias

  Computer exercises
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Revision 15
20 Jan 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Aim

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Overall aimNext Generation Sequencing (NGS) technologies allow the determination of DNA sequences from normal individuals and patients. The determination of whole-genome sequences is almost done routinely. This opens the possibility to identify mutations that cause disorders, which may lead to a further understanding of the disease, guidance of treatment selection, improved diagnostics and eventually the development of new drug. In this seminars series you will be provided with a brief introduction to DNA sequencing and how this is applied in practice. Moreover, you will analyse sequence data obtained from Nicolaides Baraitser patients to identify the mutation that causes this disease. As part of this we will point out potential difficulties in the analysis of this data. Finally, due to the very large amounts of sequence data that is being produced by NGS technologies there is an increasing need for state-of-the-art e-infrastructures that provide access to the necessary compute power. In these seminars you will get acquainted with these e-infrastructures and will learn how to get access and use them.
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Overall aim: Next Generation Sequencing (NGS) technologies allow the determination of DNA sequences from normal individuals and patients. The determination of whole-genome sequences is almost done routinely. This opens the possibility to identify mutations that cause disorders, which may lead to a further understanding of the disease, guidance of treatment selection, improved diagnostics and eventually the development of new drugs. In this seminar series you will be provided with a brief introduction to DNA sequencing and how this is applied in practice. Moreover, you will analyse sequence data obtained from Nicolaides Baraitser patients to identify the mutation that causes this disease. As part of this we will point out potential difficulties in the analysis of this data. Finally, due to the very large amounts of sequence data that are being produced by NGS technologies there is an increasing need for state-of-the-art e-infrastructures that provide access to the necessary compute power. In these seminars you will get acquainted with these e-infrastructures and will learn how to get access to them and use them.
 
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This topic is highly relevant for medical informatics. For example, the recently established Dutch Center for Genome Diagnostics is an initiative in which all UMCs participate and which aims to make mutation detection in DNA sequence part of patient care, e.g., diagnostics. This implies an increasing need to integrate results from sequence analysis and the interpretation thereof in clinical information systems to allow medical doctors and/or clinical geneticist to use such information in daily practice. Therefore, it is of importance the medical informatics professionals are aware of such developments and to become actively engaged in this field.
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This topic is highly relevant for medical informatics. For example, the recently established Dutch Center for Genome Diagnostics is an initiative in which all UMCs participate and which aims to make mutation detection in DNA sequence part of patient care, e.g., diagnostics. This implies an increasing need to integrate results from sequence analysis and the interpretation thereof in clinical information systems to allow medical doctors and/or clinical geneticist to use such information in daily practice. Therefore, it is of importance that medical informatics professionals are aware of such developments and become actively engaged in this field.
 

Course description

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Seminar 2. Bioinformatics@work 1: Identification of the gene mutation that causes Nicolaides Baraitser syndrome

Goal
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In this seminar you will analyse an exome data obtained from a Nicolaides Baraitser patient. To make this feasible, we will only use a subset of the data.
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In this seminar you will analyse exome data obtained from a Nicolaides Baraitser patient. To make this feasible, we will only use a subset of the data.
 

The data analysis is carried out in a Linux environment with the help of several applications for sequence analysis. All (Linux) commands to successfully perform the analysis will be provided to you. This will give you an impression about the actual work that needs to be done before you can start with the interpretation of the data (seminar 3) and why e-Biosciences is required for the analysis of next generation sequence data (seminar 4 and 5)
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Schedule
  • 10.00 – 11.00. Lecture. Exome sequencing and analysis (Antoine van Kampen)
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  • 11.00 – 13.00. Computer practicum. Identifications of gene mutations from exome data of Nicolaides-Baraitser (Antoine van Kampen/Perry Moerland)
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  • 11.00 – 13.00. Computer practicum. Identification of gene mutations from exome data of Nicolaides-Baraitser (Antoine van Kampen/Perry Moerland)
 
  • 13.00 - 13.45. Lunch.
  • 13.45 – 14.45. Computer practicum. Continued. (Antoine van Kampen/Perry Moerland)
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Seminar 4. e-Bioscience@work 1: e-infrastructures

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In this seminar we will introduce concepts related to e-Bioscience (), with focus on "e-infrastructures” that provide resources that enable large scale data analysis for biomedical research. First it will present an overview of state-of-the-art computing technologies used for data-intensive biomedical research, including grids, scientific workflows, and semantic web. It will also provide the opportunity for hands-on experience with the Dutch e-Science infrastructure (BiGGrid).
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In this seminar we will introduce concepts related to e-Bioscience, with focus on "e-infrastructures” that provide resources that enable large scale data analysis for biomedical research. First it will present an overview of state-of-the-art computing technologies used for data-intensive biomedical research, including grids, scientific workflows, and semantic web. It will also provide the opportunity for hands-on experience with the Dutch e-Science infrastructure (BiGGrid).
 

preliminary program
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Seminar 6. Wrap-up and borrel

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  • Presentations by students
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  • Evaluation and Closing
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  • Evaluation and closing
 

Final assignment
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  Bioinformatics Laboratory, Academic Medical Centre
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Dr. Perry Moerland
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Dr. ir. Perry Moerland
  Bioinformatics Laboratory, Academic Medical Centre
Revision 14
20 Jan 2012 - Main.AldoJongejan
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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    • Basic biology to understand DNA sequencing and analysis, e.g., DNA, exons, SNPs, basic genetics
    • OMICS
  • 11.00 -11.15. Break.
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  • 11.15 – 11.45. Lecture. Sequencing in practice: the technology (Aldo Jongejan)
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  • 11.15 – 11.45. Lecture. Sequencing in practice: the technology powerpoint (ppt)(Aldo Jongejan)
 
    • The Solid sequencer: principles
    • The data
    • Color space, fastq, bam, sam
Revision 13
20 Jan 2012 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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