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Meeting schedule - Ibivu

Meeting schedule

From Ibivu

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* The weekly meetings of the IBIVU Bioinformatics group are on <font color=red>'''Thursdays'''</font> at <font color=red>'''11:00-12:15'''</font> in room <font color=red>'''[http://www.bio.vu.nl/vakgroepen/mcp/groep/M212Res1.php M2.12]'''</font>, ''unless indicated otherwise below''. Please find the meeting schedule below.
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* The weekly meetings of the IBIVU Bioinformatics group are on <font color=red>'''Wednesdays'''</font> at <font color=red>'''11:00-12:15'''</font> in room <font color=red>'''T4.69'''</font>, ''unless indicated otherwise below''. Please find the meeting schedule below.
* The [[literature scanning scheme]] will tell you who covers which journals.
* The [[literature scanning scheme]] will tell you who covers which journals.
* Scheduled talks should be 25 minutes plus 20 minutes discussion.
* Scheduled talks should be 25 minutes plus 20 minutes discussion.
 +
* Talks should '''not be about finished work''' (that goes into the big IBIVU meeting)
 +
** highlight methodology and open problems
* The last 20 minutes are reserved for presenting breakthrough results (on the board).
* The last 20 minutes are reserved for presenting breakthrough results (on the board).
-
* If you want to schedule a presentation please contact Punto Bawono (p.bawono@vu.nl)
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* If you want to schedule a presentation please contact [mailto:p.bawono@vu.nl Punto Bawono (p.bawono@vu.nl)]
* The first meeting of every month will be the IBIVU seminar, with selected talks of members of the IBIVU (Teusink and Heringa groups, or invited speakers)
* The first meeting of every month will be the IBIVU seminar, with selected talks of members of the IBIVU (Teusink and Heringa groups, or invited speakers)
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* we will organize a separate [[Student Final Presentations Schedule|monthly session for internship presentations]]
* we will organize a separate [[Student Final Presentations Schedule|monthly session for internship presentations]]
 +
==Rotation:==
 +
 +
Regular rotation:
 +
* Ali
 +
* Nicola
 +
* Annika
 +
* Qingzhen
 +
* Erik
 +
* Maurits
 +
* Bas
 +
* Ted
 +
 +
Sporadic rotation:
 +
* Reza
 +
* Sanne
 +
* Anton
 +
* Jaap
 +
 +
==Schedule:==
 +
 +
<include iframe src="https://www.google.com/calendar/embed?mode=AGENDA&showPrint=0&showCalendars=0&wkst=2&src=N3BibjR2anJkZ25hcWV2Ym1rODk0OGFvZGtAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ&gsessionid=OK" height="600" />
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 +
* The schedule is maintained on [https://www.google.com/calendar/embed?mode=AGENDA&showPrint=0&showCalendars=0&wkst=2&src=N3BibjR2anJkZ25hcWV2Ym1rODk0OGFvZGtAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ&gsessionid=OK Google Calendar]
 +
 +
 +
==Past topics:==
{| class="wikitable sortable" class="alternategrey" cellspacing=0 cellpadding=3
{| class="wikitable sortable" class="alternategrey" cellspacing=0 cellpadding=3
-
|-
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|-
-
! Date:
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! Date:
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! Room/<br>Time:<br><small>(M212&nbsp;at&nbsp;11:00)</small>
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!
! width=170 | Speaker:
! width=170 | Speaker:
! Subject:
! Subject:
-
|- style="font-weight:bold; background-color:#ffffcc;"
 
-
| [[2012-03-29]] || M2.12 || All + Ali May || in-depth literature discussion [[Media:nmeth.1376.pdf]]
 
|-
|-
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| [[2012-04-05]] || '''F6.54''' || Huub Hoefsloot || ''Bioinformatics & Systems Biology seminar'': Integrating multivariate statistics with knowledge
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| [[2012-09-05]] || M2.12 || Hannes Hettling ||
|-
|-
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| [[2012-04-12]] || '''P4.69''' <font color=red>'''till&nbsp;12:00'''</font>
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| [[2012-06-28]] || M2.12 || All || [[literature scanning scheme|Literature]]
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|| Sanne Abeln || Introduction to NGS
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|-
 +
| [[2012-06-21]] || M2.12
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|colspan=2|
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* Alumit Mannheim: final bachelor presentation
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* Qingzhen Hou: Plan "Sequence Analysis of Homodimer and Monomer Ortholog groups"
|-
|-
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| [[2012-04-19]] || M2.12 || Nicola Bonzanni ||
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| [[2012-06-14]] || M2.12
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|colspan=2|
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* Mohammed El-Kebir
 +
* Marc Jan Bonder: mid-internship presentation
|-
|-
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| [[2012-04-26]] || M2.12 || All || [[literature scanning scheme|Literature]]
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| [[2012-06-07]] || '''F6.54''' || ''Bioinformatics & Systems Biology seminar''
-
|-
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||Maria&nbsp;Daleke & Punto Bawono: "A general secretion signal for the mycobacterial type VII secretion pathway"
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| [[2012-05-03]] || '''F6.54''' || <t.b.a.> || ''Bioinformatics & Systems Biology seminar''
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|-
-
|-
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| [[2012-05-31]] || || '''No Group meeting (due to exams)''' ||
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| [[2012-05-10]] || M2.12 || Jaap Heringa ||
+
-
|-
+
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| [[2012-05-17]] || M2.12 || Qingzhen Hou ||
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|-
|-
| [[2012-05-24]] || M2.12 || All || [[literature scanning scheme|Literature]]
| [[2012-05-24]] || M2.12 || All || [[literature scanning scheme|Literature]]
|-
|-
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| [[2012-05-31]] || '''P4.23''' || Mohammed El-Kebir ||
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| [[2012-05-17]] || || '''<ascension day>''' ||
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|-
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| [[2012-05-10]] || M2.12
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| colspan=2 |
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* ''Jaap:'' group research topics
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* ''Sanne & Anton:'' improvements, new developments and scheduling of Fundamentals of Bioinformatics (MSc) and Principles of Bioinformatics (BSc)
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||
|-
|-
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| [[2012-06-07]] || '''F6.54''' || <t.b.a.> || ''Bioinformatics & Systems Biology seminar''
+
 
 +
| [[2012-04-26]] || M2.12 || Nicola Bonzanni || Object Oriented Gene Regulatory Networks
|-
|-
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| [[2012-06-14]] || M2.12 || Punto Bawono ||
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| rowspan=3 | [[2012-04-19]]
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| rowspan=3 | M2.12
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|| Ali May || proposal defense
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|-
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|| Anton Feenstra || ''[http://www.sciencedirect.com/science/article/pii/S0022283612002951 Talavera et al. JMB 2012 - Evolvability of Yeast Protein-Protein Interaction Interfaces]''
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|-
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|| All || [[literature scanning scheme|Literature]]
|-
|-
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| [[2012-06-21]] || M2.12 || All || [[literature scanning scheme|Literature]]
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| [[2012-04-12]] || || Sanne Abeln || "The effect of denoising and clustering on 16S pyrosequencing datasets"
|-
|-
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| [[2012-06-28]] || M2.12 || Hannes Hettling ||
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| [[2012-04-05]] || || Huub Hoefsloot || ''Bioinformatics & Systems Biology seminar'': Integrating multivariate statistics with knowledge
-
|-
+
-
| [[2012-07-05]] || M2.12 || Anton Feenstra ||
+
-
|-
+
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| [[2012-07-12]] || M2.12 || All || [[literature scanning scheme|Literature]]
+
-
|-
+
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| || || '''<summer holiday>''' ||
+
-
|-
+
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| [[2012-08-23]] || M2.12 || ||
+
-
|-
+
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| [[2012-08-30]] || M2.12 || ||
+
-
|-
+
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| [[2012-09-06]] || '''<t.b.a.>''' || <t.b.a.> || ''Bioinformatics & Systems Biology seminar''
+
-
|-
+
-
|}
+
-
 
+
-
 
+
-
==Past topics:==
+
-
{| class="wikitable sortable" class="alternategrey" cellspacing=0 cellpadding=3
+
-
|-
+
-
! Date:
+
-
!
+
-
! width=170 | Speaker:
+
-
! Subject:
+
|-
|-
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| [[2012-03-22]] || M2.12 || <cancelled>
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| [[2012-03-29]] || || All + Ali May || in-depth literature discussion [[Media:nmeth.1376.pdf]]
|-
|-
| [[2012-03-15]] || || Anton Feenstra || Calculating (effective) force profiles using umbrella sampling.
| [[2012-03-15]] || || Anton Feenstra || Calculating (effective) force profiles using umbrella sampling.

Current revision

  • The weekly meetings of the IBIVU Bioinformatics group are on Wednesdays at 11:00-12:15 in room T4.69, unless indicated otherwise below. Please find the meeting schedule below.
  • The literature scanning scheme will tell you who covers which journals.
  • Scheduled talks should be 25 minutes plus 20 minutes discussion.
  • Talks should not be about finished work (that goes into the big IBIVU meeting)
    • highlight methodology and open problems
  • The last 20 minutes are reserved for presenting breakthrough results (on the board).
  • If you want to schedule a presentation please contact Punto Bawono (p.bawono@vu.nl)
  • The first meeting of every month will be the IBIVU seminar, with selected talks of members of the IBIVU (Teusink and Heringa groups, or invited speakers)

Rotation:

Regular rotation:

  • Ali
  • Nicola
  • Annika
  • Qingzhen
  • Erik
  • Maurits
  • Bas
  • Ted

Sporadic rotation:

  • Reza
  • Sanne
  • Anton
  • Jaap

Schedule:


Past topics:

Date: Speaker: Subject:
2012-09-05 M2.12 Hannes Hettling
2012-06-28 M2.12 All Literature
2012-06-21 M2.12
  • Alumit Mannheim: final bachelor presentation
  • Qingzhen Hou: Plan "Sequence Analysis of Homodimer and Monomer Ortholog groups"
2012-06-14 M2.12
  • Mohammed El-Kebir
  • Marc Jan Bonder: mid-internship presentation
2012-06-07 F6.54 Bioinformatics & Systems Biology seminar Maria Daleke & Punto Bawono: "A general secretion signal for the mycobacterial type VII secretion pathway"
2012-05-31 No Group meeting (due to exams)
2012-05-24 M2.12 All Literature
2012-05-17 <ascension day>
2012-05-10 M2.12
  • Jaap: group research topics
  • Sanne & Anton: improvements, new developments and scheduling of Fundamentals of Bioinformatics (MSc) and Principles of Bioinformatics (BSc)
2012-04-26 M2.12 Nicola Bonzanni Object Oriented Gene Regulatory Networks
2012-04-19 M2.12 Ali May proposal defense
Anton Feenstra Talavera et al. JMB 2012 - Evolvability of Yeast Protein-Protein Interaction Interfaces
All Literature
2012-04-12 Sanne Abeln "The effect of denoising and clustering on 16S pyrosequencing datasets"
2012-04-05 Huub Hoefsloot Bioinformatics & Systems Biology seminar: Integrating multivariate statistics with knowledge
2012-03-29 All + Ali May in-depth literature discussion Media:nmeth.1376.pdf
2012-03-15 Anton Feenstra Calculating (effective) force profiles using umbrella sampling.
2012-03-08 Evert Bosdriesz Bioinformatics & Systems Biology seminar
"Optimal and robust regulation of gene expression".
2012-03-01 Hannes Hettling

Continued discussion of Retrieval, alignment, and clustering of computational models based on semantic annotations by Schulz, Krause, Le Novere, Klipp, and Liebermeister (Molecular Systems Biology 2011 7:512)

2012-02-23 Leonardos Mageiros mid/end internship talk "Environment-Specific Protein Structural Alignment"
All Literature
2012-02-09
  • Marlies van der Wees: mid-internship talk
  • Punto Bawono: "Motif-aware MSA + praline"
2012-02-02 Joost Boele IBIVU seminar "PAPD5 mediates isomiR-specific adenylation of oncomiR miR-21 to induce its degradation in a novel tumor suppression pathway"
2012-01-26
  • Danielle de Man: mid-internship talk "Evolving a gene Regulatory Network"
  • All + Hannes: in-depth literature discussion Media:MSB201141.pdf
2012-01-12 Hayssam Soueidan IBIVU seminar Network reconstruction from text mining
2012-01-05 Jaap Heringa New Year's speach
2011-12-15 Nicola Bonzanni
2011-12-08
  • Ali May: mid-internship talk
  • All: Literature - in-depth AND scanning
2011-12-01

IBIVU seminar:

  • Erik van Dijk "Introducing the Hydrophobic effect in Lattice Models of Protein Folding"
  • Sanne Abeln: "Self assembly into silk fibrils"
2011-11-24 Anton Feenstra Sequence Specificity, Conservation and Protein-Protein Interactions
2011-11-03 Herwig Bachmann IBIVU seminar "Privatization of public goods leads to increased microbial efficiency but decreases growth rates"
2011-10-27 Hannes Hettling
2011-10-20 All Literature MSAProbs - Liu Schmidt Maskell 2011
2011-10-20 Bianca Mladek IBIVU Seminar "Coarse graining DNA-coated colloids" abstract
2011-10-13 Mohammed El-Kebir
2011-10-06 Brett Olivier IBIVU seminar "Stochastic Modeling"
2011-09-22 Anton Feenstra Zenith Proposal: Petri-net modeling of b-Catenin signaling
2011-09-15 Punto Bawono
2011-09-08 Nicola Bonzanni IBIVU seminar "Why stochastic modeling?"
2011-09-01 Hannes Hettling
2011-06-23 All Literature: Non-adaptive origins of interactome complexity
2011-06-09 Bernd Brandt The Fanconi / ENFANC project
+ David Vossen (Mid-internship talk)
2011-05-26 All Hogeweg's paper.
+ Michiel Vegt (Mid-internship talk)
2011-05-12 René Pool The Development of a Molecular Simulation Based Engine for the Quantification of Protein-Protein Interactions
2011-04-28 Nicola Bonzanni Google WebToolkit
2011-04-07 Pinar Ozturk
2011-03-17 All
2011-03-10 Anisha Goel
2011-03-03 Anton Feenstra SHMR: analyzing specificity in HIV disease progression and population evolution
2011-02-24 All Literature - in-depth AND scanning
2011-02-17 Sanne Protein solubility & aggregation with simple lattice models
2011-02-10 Douwe Molenaar "Probiotics"
2011-02-03 Hannes Hettling Once Again on the Functions of Creatine Kinase: the Shuttle Hypothesis
2011-01-13 Mohammed El-Kebir Network alignment
2011-01-06 Jaap Heringa New Year's speech
2010-12-02 Arjan van der Velde Distance-based alignment scoring
2010-11-25 René Pool Course-grained calculations of Protein-interaction PMF by grand-canonical MC
2010-11-18 All Shaw Science 330 15 Oct 2010 341
Science News Of The Week 330 15 Oct 2010 308
2010-11-11 Nicola Bonzanni The role of proteosome-mediated proteolysis in modulating the activity of potentially harmful transcription factor activity in Saccharomyces cerevisiae
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