## Registration

For the oral exam you need to register.

Please register here.

The information you provide will be for the Pruefungsprotokoll.

## Practical Course

USB Stick verloren? Identifiziert sich als "BIOINF LIVE". Bitte mail an

`choener@`
This year we plan to have a practical course on computational chemistry. More information soon.
Required Reading:

Catalan Game
GGL Tutorial
[PDF]
Exploration strategies paper
[PDF] (see Appendix C for the Catalan game solver)
50 Shades ... of Rule Composition
[PDF]
SMILES
Chemical reaction mechanisms (sorry, in German only)
##### Code Snippets

#### Universe / Subset Filtering

We have two filter strategies:

`filterUniverse` and

`filterSubset`. Both take a function of the type

`(Graph g,
DGStratGraphState gs, bool first) → bool`. If you want to keep

`g` in the resulting graph state, then the function needs to return

`true`, otherwise

`false`.

`gs` provides access to the
graph state (c.f.

`DGStrat` in the PyMOD manual (

`/homes/brauerei2/jlandersen/shared/doc/index.html`) (sorry, but links are rewritten by the webserver ...). The
final argument

`first` indicates that this is the first time the filter
is called for a particular round (you should be able to ignore it).

Example: keep only graphs that have few enough vertices:

`filterSubset(lambda g, gs, first: g.numVertices <= 42)`
Example: keep only graphs that have no vertix with a FAIL label:

`filterUniverse(lambda g, gs, first: g.vLabelCount("FAIL") == 0`
Example: have at most k branches in a carbon chain:

`pattern = smiles("[C][C]([C])[C]")`
`filterUniverse(lambda g, gs, first: pattern.monomorphism(g, maxNumMatches=k + 1) <= k)`
##### Killing MOL

Send the running MOL to sleep with

`CTRL+Z`. Then kill python with

`pkill python3`. Be VERY careful as you will kill all MOLs of all people.

## Lecture

The lecture was a blackboard-style lecture. There is no TeX script!

## Seminar

papers with graph-theoretic content from the past 12 months (approximately): graph theory papers or bioinformatics with graph theory content
not obviously trivial. I will *at most* do a 1-minute check, and not provide any guarantees.
first email in (*according to my inbox time stamp*) counts at choener@bioinf
send me one paper title, I won't select for you
use a meaningful email subject header, maybe "Graphen + BioNetze, Seminar, 2015, Paper"
if you don't get a mail / paper doesn't show up after a couple of *work* days (say 3) send a gentle reminder

#### Seminar Program

** TUESDAY 23.Feb 10:30-13:00 Session 1: Graph Properties**
[J Anders] Tropical Dominating Sets in Vertex-Coloured Graphs ; 2015 ; arxiv ; Angles d'Auriac et al
[T Mueller] Robust on-line computation of Reeb graphs: simplicity and speed ; 2007 ; siggraph 07 ; Pascucci et al
[S Zoetzsche] Easily Testable Graph Properties; 2015; Comb.Prob.Comp.; Alon, Fox
[F Raith] Graph theory in the geosciences ; 2015 ; Earth-Science Reviews ; Phillips et al
[M Fuhrmann] The vertex-rainbow index of a graph ; 2015 ; arxvi ; Mao
**THURSDAY 25.Feb 10:30-12:30 & 14:00-16:00 Session 2: Neuro-Applications**
[F Reinhardt] Graph Theoretical Analysis Reveals: Womens Brains Are Better Connected than Mens ; 2015 ; Plos One ; Szalkai et al
[O Scheer] Graph theory analysis of complex brain networks: new concepts in brain mapping applied to neurosurgery ; 2015 ; JNS ; Hart et al
[P Nardini] Subvoxel Accurate Graph Search Using Non-Euclidean Graph Space ; 2014 ; Plos One ; Abramoff et al
[J Huebner] Changes of Functional Brain Networks in Major Depressive Disorder: A Graph Theoretical Analysis of Resting-State fMRI ; 2015 ; Plos One ; Ye et al
**lunch break**
[E Mueller] Dynamic reorganization of brain functional networks during cognition ; 2015 ; NeuroImage ; Bola et al
[U Klotz] A Graph Algorithmic Approach to Separate Direct from Indirect Neural Interactions ; 2015 ; Plos One ; Wollstadt et al
[Y Peng] Functional connectivity and graph theory in preclinical Alzheimer's disease; 2014 ; Neurobiology of Aging ; Brier et al
[S Rauh] Non-invasive brain mapping in epilepsy: Applications from magnetoencephalography; 2015; J of Neuroscience Methods; Hamandi et al
** THURSDAY 25.Feb 16:30-17:30 Session 3: Applications in Soft Computing**
[A Murad] Causal analysis approaches in Ingenuity Pathway Analysis; 2014; oup bioinf; Kraemer at al
[K Hainke] A Divide-and-Link algorithm for hierarchical clustering in networks; 2015; Information Sciences; Gomez et al
** FRIDAY 26.Feb 10:30-12:30 & 14:00-16:00 Session 4: Genomics and Regulation**
[C Schimmelpfennig] Graphical pan-genome analysis with compressed suffix trees and the Burrowsâ€“Wheeler transform ; 2015 ; Bioinformatics ; Uwe Baier, Timo Beller and Enno Ohlebusch
[R Toscan] Some Perspectives on Network Modeling in Therapeutic Target Prediction ; 2014 ; Biomedical Engineering and Computational Biology ; Albert et al
[M Rade] BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference ; 2015 ; BMC BioInf ;AureIlie Pirayre et al.
[M Schmidt] Optimal Learning Paths in Information Networks ; 2015 ; Scientific Reports ; Rodi et al
**lunch break**
[J Fusiak] BulkAligner: A novel sequence alignment algorithm based on graph theory and Trinity; 2015; Information sciences; Lee at al
[S Johanning] The Roles of Sharing, Transfer, and Public Funding in Nanotechnology Knowledge-Diffusion Networks; 2015 ; JAIST; Jiang et al
[L Lijing] Factor graph analysis of live cellâ€“imaging data reveals mechanisms of cell fate decisions; 2015; Bioimape Inf. ; Niederberger et al
[D Gysi] Comparing Brain Networks of Different Size and Connectivity Density Using Graph Theory; 2010; van Wijk et al
**Nachzuegler**
[M Gauglitz] Ion aggregation in high salt solutions. IV. Graph-theoretical analyses of ion aggregate structure and water hydrogen bonding network; 2015; Choi and Cho