Difference: EducationMIKSeminars2013 (1 vs. 20)

Revision 20
29 Sep 2014 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
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Medical Bioinformatics

 
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  In this seminar your will be introduced to Next Generation Sequencing (NGS) and, in particular, exome sequencing. These introductions will provide you with some basic understanding of these technologies and their applications.

Schedule
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  • 10.00 – 10.30. Lecture. Introduction to the module (Antoine van Kampen)
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  • 10.00 - 10.30. Lecture. Introduction to the module (Antoine van Kampen)
 
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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 powerpoint (ppt) (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
    • Introduction some basic tooling bwa, samtools
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  • 11.45 – 13.15 Lunch
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  • 11.45 - 13.15 Lunch
 
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  • 13.15 – 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Barbera van Schaik)
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  • 13.15 - 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Barbera van Schaik)
 
    • Genome and exome sequencing
    • The story of Nicholas Volker (video)
    • Human Genome Projects
    • Genome of the Netherlands, 1k, 10k genome projects
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  • 13.45 – 14.45. Computer practicum: sequence databases and online visualization/analysis tools (Antoine van Kampen)
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  • 13.45 - 14.45. Computer practicum: sequence databases and online visualization/analysis tools (Antoine van Kampen)
 
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Schedule
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  • 10.00 – 11.00. Lecture. Exome sequencing and analysis (Barbera van Schaik)
  • 11.00 – 13.00. Computer practicum. Identification of gene mutations from exome data of Nicolaides-Baraitser (Barbera van Schaik)
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  • 10.00 - 11.00. Lecture. Exome sequencing and analysis (Barbera van Schaik)
  • 11.00 - 13.00. Computer practicum. Identification of gene mutations from exome data of Nicolaides-Baraitser (Barbera van Schaik)
 
  • 13.00 - 13.45. Lunch.
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  • 13.45 – 14.45. Computer practicum. Continued. (Barbera van Schaik)
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  • 13.45 - 14.45. Computer practicum. Continued. (Barbera van Schaik)
 

Background information
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Schedule
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  • 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)
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  • 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.
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  • 13.45 – 15.00. Computer practicum. Continued. (Perry Moerland)
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  • 13.45 - 15.00. Computer practicum. Continued. (Perry Moerland)
 

Background information
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11 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Background information
Revision 18
11 Jan 2013 - Main.BarberaVanSchaik
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Revision 17
11 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • 12:30 - 13:15 Lunch
  • 13.15 - 15:15 Practical exercises (Barbera van Schaik, Mark Santcroos, Silvia Olabarriaga)
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Revision 16
10 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Background information
Revision 15
10 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • Guide to e-Science Next Generation Scientific Research and Discovery, Springer, 2011.
  • see many links in the slides
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register your gateway account Please register before 16:00 today (else you wont have an account for the practical exercises later on!)
 

Seminar 5. e-Bioscience @work: Usage of e-infrastructures

IIn this seminar we will present how e-infrastructures are used in practice based on scientific workflow management technology. The major concepts will be introduced, and we will show these are implemented in practice in the e-science platform used at the AMC (e-bionfra). These concepts will be then illustrated in two manners. Firstly, a guest speaker will present how the e-bioinfra and other Dutch e-infrastructure resources are used in practice for the analysis of sequencing data at the AMC. Secondly, during the practice the students will have hands-on experience with one workflow management system. Additionally, an invited speaker will present how high-performance computing applications (for protein research) can be offered as a service
Revision 14
10 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • see many links in the slides
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register your gateway account Please register before 16:00 today (else you wont have an account for the practical exercises later on!)
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register your gateway account Please register before 16:00 today (else you wont have an account for the practical exercises later on!)
 

Seminar 5. e-Bioscience @work: Usage of e-infrastructures

Revision 13
10 Jan 2013 - MarkSantcroos
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Background information
Revision 12
10 Jan 2013 - MostaphaAlMourabit
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • Guide to e-Science Next Generation Scientific Research and Discovery, Springer, 2011.
  • see many links in the slides
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register your gateway account Please register before 16:00 today (else you wont have an account for the practical exercises later on!)
 

Seminar 5. e-Bioscience @work: Usage of e-infrastructures

IIn this seminar we will present how e-infrastructures are used in practice based on scientific workflow management technology. The major concepts will be introduced, and we will show these are implemented in practice in the e-science platform used at the AMC (e-bionfra). These concepts will be then illustrated in two manners. Firstly, a guest speaker will present how the e-bioinfra and other Dutch e-infrastructure resources are used in practice for the analysis of sequencing data at the AMC. Secondly, during the practice the students will have hands-on experience with one workflow management system. Additionally, an invited speaker will present how high-performance computing applications (for protein research) can be offered as a service
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09 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Background information
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09 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Course description

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Schedule

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Background information
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  • see many links in the slides

Seminar 5. e-Bioscience @work: Usage of e-infrastructures

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In this seminar we will present how e-infrastructures are used in practice based on scientific workflow management technology. The major concepts will be introduced, and we will show these are implemented in practice in the e-science platform used at the AMC (e-boinfra). These concepts will be then illustrated in two manners. Firstly, a guest speaker will present how the e-bioinfra and other Dutch e-infrastructure resources are used in practice for the analysis of sequencing data at the AMC. Secondly, during the practice the students will have hands-on experience with one workflow management system.
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IIn this seminar we will present how e-infrastructures are used in practice based on scientific workflow management technology. The major concepts will be introduced, and we will show these are implemented in practice in the e-science platform used at the AMC (e-bionfra). These concepts will be then illustrated in two manners. Firstly, a guest speaker will present how the e-bioinfra and other Dutch e-infrastructure resources are used in practice for the analysis of sequencing data at the AMC. Secondly, during the practice the students will have hands-on experience with one workflow management system. Additionally, an invited speaker will present how high-performance computing applications (for protein research) can be offered as a service
 

Schedule (morning lectures in room L0-218-2 and afternoon practice in room L0-227)

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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)
  • Shahand S, Santcroos M, van Kampen AHC, Olabarriaga SD. A Grid-enabled Gateway for Biomedical Data Analysis. Journal of Grid Computing, December 2012, Volume 10, Issue 4, pp 725-742 (abstract)
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  • Barbera D C van Schaik, Mark Santcroos, Vladimir Korkhov, Aldo Jongejan, Marcel Willemsen, Antoine H C van Kampen, Silvia D Olabarriaga (2012) Challenges in DNA sequence analysis on a production grid In: PoS (EGICF12-EMITC2)039 1-19 (pdf)
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  • Barbera D C van Schaik, Mark Santcroos, Vladimir Korkhov, Aldo Jongejan, Marcel Willemsen, Antoine H C van Kampen, Silvia D Olabarriaga (2012) Challenges in DNA sequence analysis on a production grid In: PoS (EGICF12-EMITC2)039 1-19 (pdf)
 
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08 Jan 2013 - Main.BarberaVanSchaik
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Presentation
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Computer exercises
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08 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Course description

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Schedule

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

In this seminar we will introduce concepts related to e-bioscience, which is a new approach to carry out large scale and collaborative biomedical research using advanced computing infrastructures (e-infrastructures).
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After presenting general concepts, the seminar will focus on practical aspects and examples of e-infrastructures worldwide and in The Netherlands. During the practice the students will see behind the scenes of the cloud and grid Dutch e-Science infrastructure, and reflect upon the infrastructure needed to support a hypothetical research project.
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After presenting general concepts, the seminar will focus on practical aspects and examples of e-infrastructures in NL and worldwide. During the practice the students will see behind the scenes of cloud and grid computing on the Dutch e-Science infrastructure, and reflect upon the infrastructure needed to support a hypothetical research project.
 
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Schedule
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Schedule (morning lectures in room L0-218-2 and afternoon practice in room L0-230)
 
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  • 12:30 - 13:15 Lunch
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  • 13.15 – 15:15 Practical exercises in Room L0-230 (Barbera van Schaik, Mark Santcroos, Silvia Olabarriaga)
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Background information
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  • see also many links in the slides
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  • see many links in the slides

Seminar 5. e-Bioscience @work: Usage of e-infrastructures

In this seminar we will present how e-infrastructures are used in practice based on scientific workflow management technology. The major concepts will be introduced, and we will show these are implemented in practice in the e-science platform used at the AMC (e-boinfra). These concepts will be then illustrated in two manners. Firstly, a guest speaker will present how the e-bioinfra and other Dutch e-infrastructure resources are used in practice for the analysis of sequencing data at the AMC. Secondly, during the practice the students will have hands-on experience with one workflow management system.

Schedule (morning lectures in room L0-218-2 and afternoon practice in room L0-227)

 
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Seminar 5. e-Bioscience @work: usage of e-infrastructures for DNA Analysis

 
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to be announced
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Background information

  • 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)
  • Shahand S, Santcroos M, van Kampen AHC, Olabarriaga SD. A Grid-enabled Gateway for Biomedical Data Analysis. Journal of Grid Computing, December 2012, Volume 10, Issue 4, pp 725-742 (abstract)
  • Barbera D C van Schaik, Mark Santcroos, Vladimir Korkhov, Aldo Jongejan, Marcel Willemsen, Antoine H C van Kampen, Silvia D Olabarriaga (2012) Challenges in DNA sequence analysis on a production grid In: PoS (EGICF12-EMITC2)039 1-19 (pdf)
  • Hunting viruses on a haystack (isgtw)
  • see also many links in the slides
 

Revision 7
07 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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

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In this seminar we will introduce concepts related to e-bioscience, which is a new approach to carry out large scale and collaborative biomedical research using advanced computing infrastructures (e-infrastructures). After presenting general concepts, the seminar will focus on practical aspects and examples of e-infrastructures worldwide and in The Netherlands. During the practice the students will see behind the scenes of the cloud and grid Dutch e-Science infrastructure, and reflect upon the infrastructure needed to support a hypothetical research project.

Schedule

  • 09.30 - 10.30 Lecture: e-science: motivation and scope (Silvia Olabarriaga)
  • 10.30 - 11.30 Lecture: e-infrastructures (Silvia Olabarriaga)
  • 11:30 - 12:30 Lecture: Overview of the Dutch e-science infrastructure (Jan Bot, SURFSara)
  • 12:30 - 13:15 Lunch
  • 13.15 – 15:15 Practical exercises in Room L0-230 (Barbera van Schaik, Mark Santcroos, Silvia Olabarriaga)

Background information
  • see also many links in the slides
 
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Seminar 5. e-Bioscience @work 2: usage of e-infrastructures for DNA Analysis

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Seminar 5. e-Bioscience @work: usage of e-infrastructures for DNA Analysis

 

to be announced
Revision 6
07 Jan 2013 - Main.BarberaVanSchaik
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • 11.45 – 13.15 Lunch
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  • 13.15 – 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Barbera van Schaik)
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  • 13.15 – 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Barbera van Schaik)
 
    • Genome and exome sequencing
    • The story of Nicholas Volker (video)
    • Human Genome Projects
Revision 5
05 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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

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Seminar 4. e-Bioscience@work: 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. 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.

Schedule

Background information

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

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.

Background information

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to be announced
 
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Seminar 5. e-Bioscience @work 2: usage of e-infrastructures for DNA Analysis

 
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to be announced
 

Revision 4
02 Jan 2013 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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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.
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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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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 an e-science approach is required for the analysis of next generation sequence data (seminars 4 and 5)
 

Schedule
Revision 3
22 Dec 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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MIK Bachelor Seminars 2012: From DNA to Patient Care
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MIK Bachelor Seminars 2013: From DNA to Patient Care
 
Teachers
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Aim

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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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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 that medical informatics professionals are aware of such developments and 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 sequences 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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Schedule

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Seminar 1. From DNA to diagnostics: setting the context

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    • The data
    • Color space, fastq, bam, sam
    • Introduction some basic tooling bwa, samtools
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  • 11.45 – 12.15 Lab visit. Sequencing facility (Frank Baas)
 
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  • 12.15 – 13.15 Lunch
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  • 11.45 – 13.15 Lunch
 
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  • 13.15 – 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Antoine van Kampen)
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  • 13.15 – 13.45 Lecture. Genome / exome sequencing in patient care powerpoint (pptx) (Barbera van Schaik)
 
    • Genome and exome sequencing
    • The story of Nicholas Volker (video)
    • Human Genome Projects
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Schedule
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  • 10.00 – 11.00. Lecture. Exome sequencing and analysis (Antoine van Kampen)
  • 11.00 – 13.00. Computer practicum. Identification of gene mutations from exome data of Nicolaides-Baraitser (Antoine van Kampen/Perry Moerland)
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  • 10.00 – 11.00. Lecture. Exome sequencing and analysis (Barbera van Schaik)
  • 11.00 – 13.00. Computer practicum. Identification of gene mutations from exome data of Nicolaides-Baraitser (Barbera van Schaik)
 
  • 13.00 - 13.45. Lunch.
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  • 13.45 – 14.45. Computer practicum. Continued. (Antoine van Kampen/Perry Moerland)
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  • 13.45 – 14.45. Computer practicum. Continued. (Barbera van Schaik)
 

Background information
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The story of Nicholas Volker
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Presentation
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Schedule
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Background information
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  • see also many links in the slides

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

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.
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  • 11:30 - 12:30 Lectures: Analysis of genomics data 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)
Revision 2
20 Dec 2012 - Main.SilviaOlabarriaga
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  Bioinformatics Laboratory, Academic Medical Centre
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Shayan Shahand
Bioinformatics Laboratory, Academic Medical Centre

Tom Visser
SARA, BiGGrid

Dr. Lia van der Hoek
Virus Discovery Lab, Academic Medical Centre
 .

 
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