Meeting schedule
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- | * The weekly meetings of the IBIVU Bioinformatics group are on <font color=red>''' | + | * 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 | ||
|- | |- | ||
- | + | ! Date: | |
- | + | ! | |
- | + | ! width=170 | Speaker: | |
- | + | ! Subject: | |
|- | |- | ||
- | | [[2012- | + | | [[2012-09-05]] || M2.12 || Hannes Hettling || |
- | | | + | |
- | + | ||
- | + | ||
|- | |- | ||
- | | [[2012- | + | | [[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" | ||
|- | |- | ||
- | | [[ | + | | [[2012-06-14]] || M2.12 |
+ | |colspan=2| | ||
+ | * Mohammed El-Kebir | ||
+ | * Marc Jan Bonder: mid-internship presentation | ||
|- | |- | ||
- | | [[2012- | + | | [[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 scanning scheme|Literature]] |
|- | |- | ||
- | | [[ | + | | [[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) | ||
+ | || | ||
|- | |- | ||
- | | [[ | + | |
+ | | [[2012-04-26]] || M2.12 || Nicola Bonzanni || Object Oriented Gene Regulatory Networks | ||
|- | |- | ||
- | | [[ | + | | 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]] | ||
|- | |- | ||
- | | [[ | + | | [[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 <br>"''[[2012-03-08 IBIVU Evert Bosdriesz|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) | ||
|- | |- | ||
- | + | | rowspan=2 | [[2012-02-23]] | |
- | + | | rowspan=2 | | |
- | | [[2012- | + | || Leonardos Mageiros || mid/end internship talk "''Environment-Specific Protein Structural Alignment''" |
- | + | |- | |
+ | || All || [[literature scanning scheme|Literature]] | ||
|- | |- | ||
- | | [[2012-01-26]] || | + | | [[2012-02-09]] || |
+ | | colspan=2 | | ||
+ | * 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]] || | ||
| colspan=2 | | | colspan=2 | | ||
* Danielle de Man: mid-internship talk "Evolving a gene Regulatory Network" | * Danielle de Man: mid-internship talk "Evolving a gene Regulatory Network" | ||
* All + Hannes: in-depth literature discussion [[Media:MSB201141.pdf]] | * All + Hannes: in-depth literature discussion [[Media:MSB201141.pdf]] | ||
- | |||
- | |||
|- | |- | ||
| [[2012-01-12]] || || Hayssam Soueidan || IBIVU seminar ''Network reconstruction from text mining'' | | [[2012-01-12]] || || Hayssam Soueidan || IBIVU seminar ''Network reconstruction from text mining'' |
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)
- we will organize a separate monthly session for internship presentations
Rotation:
Regular rotation:
- Ali
- Nicola
- Annika
- Qingzhen
- Erik
- Maurits
- Bas
- Ted
Sporadic rotation:
- Reza
- Sanne
- Anton
- Jaap
Schedule:
- The schedule is maintained on Google Calendar
Past topics:
Date: | Speaker: | Subject: | ||
---|---|---|---|---|
2012-09-05 | M2.12 | Hannes Hettling | ||
2012-06-28 | M2.12 | All | Literature | |
2012-06-21 | M2.12 |
| ||
2012-06-14 | M2.12 |
| ||
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 |
| ||
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 |
| |||
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 |
| |||
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 |
| |||
2011-12-01 |
IBIVU seminar:
| |||
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 |