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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 [[collective 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 [mailto:p.bawono@vu.nl Punto Bawono (p.bawono@vu.nl)]
-
* The first meeting of every month will be the IBIVU seminar, with two selected talks of members of the IBIVU (Teusink and Heringa groups)
+
* 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)
-
{| class="wikitable sortable"
+
* 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
 +
|-
 +
! Date:
 +
!
 +
! width=170 | Speaker:
 +
! Subject:
 +
|-
 +
| [[2012-09-05]] || M2.12 || Hannes Hettling ||
 +
|-
 +
| [[2012-06-28]] || M2.12 || All || [[literature scanning scheme|Literature]]
|-
|-
-
! Date: !! Room/<br>Time:<br><small>(M212 at<br> 11:00)</small> !! Speaker: !! Subject:
+
| [[2012-06-21]] || M2.12
-
|- style="font-weight:bold; background-color:#ffffcc;"
+
|colspan=2|
-
| [[2011-09-01]] || S623 || Nicola&nbsp;Bonzanni ''and'' Brett&nbsp;Olivier || IBIVU seminar "''stochastic modeling''"
+
* Alumit Mannheim: final bachelor presentation
 +
* Qingzhen Hou: Plan "Sequence Analysis of Homodimer and Monomer Ortholog groups"
|-
|-
-
| [[2011-09-08]] || || All || Literature - in-depth AND [[collective literature scanning scheme|scanning]] ||
+
| [[2012-06-14]] || M2.12
 +
|colspan=2|
 +
* Mohammed El-Kebir
 +
* Marc Jan Bonder: mid-internship presentation
|-
|-
-
| [[2011-09-15]] || || Punto&nbsp;Bawono ||
+
| [[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)''' ||
|-
|-
-
| [[2011-09-22]] || || Jaap&nbsp;Heringa ||
+
| [[2012-05-24]] || M2.12 || All || [[literature scanning scheme|Literature]]
|-
|-
-
| [[2011-09-29]] || || All || Literature - in-depth AND [[collective literature scanning scheme|scanning]]
+
| [[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)
 +
||
|-
|-
-
| [[2011-10-06]] || || Mohammed&nbsp;El-Kebir ||
+
 
 +
| [[2012-04-26]] || M2.12 || Nicola Bonzanni || Object Oriented Gene Regulatory Networks
|-
|-
-
| [[2011-10-13]] || || Hannes&nbsp;Hettling ||
+
| rowspan=3 | [[2012-04-19]]
 +
| rowspan=3 | M2.12
 +
|| Ali May || proposal defense
 +
|-
 +
|| Anton Feenstra || ''[http://www.sciencedirect.com/science/article/pii/S0022283612002951 Talavera et al. JMB 2012 - Evolvability of Yeast Protein-Protein Interaction Interfaces]''
 +
|-
 +
|| All || [[literature scanning scheme|Literature]]
|-
|-
-
| [[2011-10-20]] || <font color=red>'''????'''</font>
+
| [[2012-04-12]] || || Sanne Abeln || "The effect of denoising and clustering on 16S pyrosequencing datasets"
-
|| All || Literature - in-depth AND [[collective literature scanning scheme|scanning]]
+
|-
|-
-
| [[2011-10-27]] || || Anton&nbsp;Feenstra
+
| [[2012-04-05]] || || Huub Hoefsloot || ''Bioinformatics & Systems Biology seminar'': Integrating multivariate statistics with knowledge
|-
|-
-
| [[2011-11-03]] || C629 || <t.b.d> || IBIVU seminar
+
| [[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.
|-
|-
-
| [[2011-11-10]] || || All || Literature - in-depth AND [[collective literature scanning scheme|scanning]]
+
| [[2012-03-08]] || || Evert Bosdriesz || Bioinformatics & Systems Biology seminar <br>"''[[2012-03-08 IBIVU Evert Bosdriesz|Optimal and robust regulation of gene expression]]''".
|-
|-
-
| [[2011-11-17]] || || Sanne&nbsp;Abeln
+
| [[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)
|-
|-
-
| [[2011-11-24]] || || Nicola&nbsp;Bonzanni
+
| rowspan=2 | [[2012-02-23]]
 +
| rowspan=2 |
 +
|| Leonardos Mageiros || mid/end internship talk "''Environment-Specific Protein Structural Alignment''"
 +
|-
 +
|| All || [[literature scanning scheme|Literature]]
|-
|-
-
| [[2011-12-01]] || || All || Literature - in-depth AND [[collective literature scanning scheme|scanning]]
+
| [[2012-02-09]] ||
 +
| colspan=2 |
 +
* Marlies&nbsp;van&nbsp;der&nbsp;Wees: mid-internship talk
 +
* Punto&nbsp;Bawono: "Motif-aware MSA + praline"
 +
|-
|-
|-
-
| [[2011-12-08]] || ||
+
| [[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"''
|-
|-
-
| [[2011-12-15]] || ||
+
| [[2012-01-26]] ||
 +
| colspan=2 |
 +
* Danielle&nbsp;de&nbsp;Man: mid-internship talk "Evolving a gene Regulatory Network"
 +
* All + Hannes: in-depth literature discussion [[Media:MSB201141.pdf]]
|-
|-
-
|}
+
| [[2012-01-12]] || || Hayssam&nbsp;Soueidan || IBIVU seminar ''Network reconstruction from text mining''
-
 
+
|-
 +
| [[2012-01-05]] || || Jaap&nbsp;Heringa || New Year's speach
 +
|-
 +
| [[2011-12-15]] || || Nicola&nbsp;Bonzanni
 +
|-
 +
| [[2011-12-08]] ||
 +
| colspan=2 |
 +
* Ali&nbsp;May: mid-internship talk
 +
* All: Literature - in-depth AND [[literature scanning scheme|scanning]]
 +
|-
 +
| [[2011-12-01]] ||
 +
| colspan=3 |
 +
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&nbsp;Feenstra || Sequence Specificity, Conservation and Protein-Protein Interactions
 +
|-
 +
| [[2011-11-03]] || || Herwig&nbsp;Bachmann || IBIVU seminar ''"Privatization of public goods leads to increased microbial efficiency but decreases growth rates"''
 +
|-
 +
| [[2011-10-27]] || || Hannes&nbsp;Hettling
 +
|-
 +
| [[2011-10-20]] || || All || Literature [[Media:MSAProbs - Liu Schmidt Maskell 2011.pdf|MSAProbs - Liu Schmidt Maskell 2011]]
-
==Past topics:==
+
|-
-
{| class="wikitable sortable"
+
| [[2011-10-20]] || || Bianca&nbsp;Mladek || IBIVU Seminar ''"Coarse graining DNA-coated colloids"'' [[2011-10-20 Bianca Mladek | abstract]]
-
|-
+
|-
-
! Date: !! !! Speaker: !! Subject:
+
| [[2011-10-13]] || || Mohammed&nbsp;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&nbsp;Bawono ||
 +
|-
 +
| [[2011-09-08]] || || Nicola&nbsp;Bonzanni || IBIVU seminar "''Why stochastic modeling?''"
 +
|-
 +
| [[2011-09-01]] || || Hannes Hettling ||
|-
|-
| [[2011-06-23]] || || All || Literature: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09992.html Non-adaptive origins of interactome complexity]
| [[2011-06-23]] || || All || Literature: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09992.html Non-adaptive origins of interactome complexity]
Line 76: Line 183:
| [[2011-03-03]] || || Anton&nbsp;Feenstra || SHMR: analyzing specificity in HIV disease progression and population evolution
| [[2011-03-03]] || || Anton&nbsp;Feenstra || SHMR: analyzing specificity in HIV disease progression and population evolution
|-
|-
-
| [[2011-02-24]] || || All || Literature - in-depth AND [[collective literature scanning scheme|scanning]]
+
| [[2011-02-24]] || || All || Literature - in-depth AND [[literature scanning scheme|scanning]]
|-
|-
| [[2011-02-17]] || || Sanne || Protein solubility & aggregation with simple lattice models
| [[2011-02-17]] || || Sanne || Protein solubility & aggregation with simple lattice models

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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