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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.
+
* 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)
+
* 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)
 +
* 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" />
 +
 +
* 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
-
|-
+
|-
-
! Date:
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! Date:
-
! 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;"
 
-
| [[2012-03-15]] || M2.12 || Anton Feenstra ||
 
|-
|-
-
| [[2012-03-22]] || M2.12 || Sanne Abeln ||
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| [[2012-09-05]] || M2.12 || Hannes Hettling ||
|-
|-
-
| [[2012-03-29]] || M2.12 || All || [[literature scanning scheme|Literature]]
+
| [[2012-06-28]] || M2.12 || All || [[literature scanning scheme|Literature]]
 +
|-
 +
| [[2012-06-21]] || M2.12
 +
|colspan=2|
 +
* Alumit Mannheim: final bachelor presentation
 +
* Qingzhen Hou: Plan "Sequence Analysis of Homodimer and Monomer Ortholog groups"
|-
|-
-
| [[2012-04-05]] || F6.54 || Huub Hoefsloot || Bioinformatics & Systems Biology seminar
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| [[2012-06-14]] || M2.12
 +
|colspan=2|
 +
* Mohammed El-Kebir
 +
* Marc Jan Bonder: mid-internship presentation
|-
|-
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| [[2012-04-12]] || M2.12 || Nicola Bonzanni ||
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| [[2012-06-07]] || '''F6.54''' || ''Bioinformatics & Systems Biology seminar''
 +
||Maria&nbsp;Daleke & Punto Bawono: "A general secretion signal for the mycobacterial type VII secretion pathway"
 +
|-
 +
| [[2012-05-31]] || || '''No Group meeting (due to exams)''' ||
|-
|-
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| [[2012-04-19]] || M2.12 || Jaap Heringa ||
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| [[2012-05-24]] || M2.12 || All || [[literature scanning scheme|Literature]]
|-
|-
-
| [[2012-04-26]] || M2.12 || All || [[literature scanning scheme|Literature]]
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| [[2012-05-17]] || || '''<ascension day>''' ||
 +
|-
 +
| [[2012-05-10]] || M2.12
 +
| colspan=2 |
 +
* ''Jaap:'' group research topics
 +
* ''Sanne & Anton:'' improvements, new developments and scheduling of Fundamentals of Bioinformatics (MSc) and Principles of Bioinformatics (BSc)
 +
||
|-
|-
-
| [[2012-05-03]] || 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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| [[2012-05-10]] || M2.12 || Qingzhen Hou ||
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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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|| 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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|| All || [[literature scanning scheme|Literature]]
|-
|-
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| [[2012-05-17]] || M2.12 || Mohammed El-Kebir ||
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| [[2012-04-12]] || || Sanne Abeln || "The effect of denoising and clustering on 16S pyrosequencing datasets"
|-
|-
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| [[2012-05-24]] || M2.12 || All || [[literature scanning scheme|Literature]]
+
| [[2012-04-05]] || || Huub Hoefsloot || ''Bioinformatics & Systems Biology seminar'': Integrating multivariate statistics with knowledge
-
|-
+
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| [[2012-05-31]] || M2.12 || Punto Bawono ||
+
-
|-
+
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| [[2012-06-07]] || M2.12 || Hannes Hettling ||
+
|-
|-
-
|}
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| [[2012-03-29]] || || All + Ali May || in-depth literature discussion [[Media:nmeth.1376.pdf]]
-
 
+
-
 
+
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==Past topics:==
+
-
{| class="wikitable sortable" class="alternategrey" cellspacing=0 cellpadding=3
+
-
|-
+
-
! Date:
+
-
!
+
-
! width=170 | Speaker:
+
-
! Subject:
+
|-
|-
-
| [[2012-03-08]] || C6.59 || Evert Bosdriesz || Bioinformatics & Systems Biology seminar <br>"''[[2012-03-08 IBIVU Evert Bosdriesz|Optimal and robust regulation of gene expression]]''".
+
| [[2012-03-15]] || || Anton Feenstra || Calculating (effective) force profiles using umbrella sampling.
 +
|-
 +
| [[2012-03-08]] || || Evert Bosdriesz || Bioinformatics & Systems Biology seminar <br>"''[[2012-03-08 IBIVU Evert Bosdriesz|Optimal and robust regulation of gene expression]]''".
|-
|-
-
| [[2012-03-01]] || C6.24 || Hannes Hettling ||
+
| [[2012-03-01]] || || Hannes Hettling ||
Continued discussion of ''Retrieval, alignment, and clustering of computational
Continued discussion of ''Retrieval, alignment, and clustering of computational
models based on semantic annotations'' by Schulz, Krause, Le Novere,
models based on semantic annotations'' by Schulz, Krause, Le Novere,
Line 59: Line 100:
|-
|-
| rowspan=2 | [[2012-02-23]]
| rowspan=2 | [[2012-02-23]]
-
| rowspan=2 | M2.12
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| rowspan=2 |
-
|| Leonardos Mageiros || mid/end internship talk "'''Environment-Specific Protein Structural Alignment'''"
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|| Leonardos Mageiros || mid/end internship talk "''Environment-Specific Protein Structural Alignment''"
|-
|-
|| All || [[literature scanning scheme|Literature]]
|| All || [[literature scanning scheme|Literature]]

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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