Python for standalone

applications
Stefanie Lck
 Software situation in life science for
high throughput applications
Rarely with graphical user interface(command line
only)
Usually run on Unix/Linux servers and require
assistance
No offline support
No custom database support
 Pathogen-Stress Genomics lab
Leibniz Institute of Plant Genetics and Crop Plant Research
Barley - powdery mildew as a model
for plant-pathogen interactions

Which
genes
are
important
?

Resistant Susceptible
Healthy barley Powdery mildew
infected barley
 A typical life science lab workflow

Data mining
Sequence Analysis of
& gene
analysis results
discovery

Each step requires different software!

 Software Requirements

Small and easy to use applications for specific

needs in the lab
Software development with user-friendly graphical
interface
o Python & PyQT

Shipped with Windows Installer

o py2exe & Inno Setup

Current status:
Five programs released, two in progress
All support offline mode
All support custom database (if required)
All support single and batch mode (if required)
At the moment Windows only, Linux planned
 Software presented in this talk

Blaster Tool for alignment, extraction and

manipulation of sequences
siFi21 RNAi off-target prediction and RNAi design
tool
Anno - An image browser for annotating
microscopic images
 Data mining & gene discovery

Blaster
Tool for alignment, extraction and
manipulation of nucleic acid sequences
 Data mining & gene discovery

Typical tasks
Sequence Translation Sequence Alignment
CCCTGCAAATGCTCATGCTCA CCCTGCTAATGCTGATGCTGAT
P C K C S C S CCC-GCTAA-GCTG-TGCTGAT

Excel,
Web applications,
Software packages,
cmd
Sequence Extraction
Sequence Search
<MySequence01
CCCTGCTAATGCTGATGCTGAT
ATGCTGATCGCGTCGCTCGCTGAGT
GGTAGCTTATGCTCGCGGCTCT
<MySequence02
CATGCTCGCTTAGCCGCTCGGC
ATGCTGATCGCGTCGCGCGA
ATGCTCGCCTCGGTATTCGCTC
 Data mining & gene discovery

Blaster Features
Provides GUI for three popular cmd tools
Support two sequence similarity search algorithms
o BLAST1 (heuristic approach)
o BOWTIE2 (short sequences, BurrowsWheeler transform)

Sequence extractions from files

Sequence conversion/translation (DNA, RNA,
Protein)
Custom database management
Offline support (data confidentiality)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410
2. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
Data mining & gene discovery

Blaster Screenshots

http://www.snowformatics.com/blaster.html
 Sequence analysis

siFi21
RNA interference (RNAi) off-target
prediction and RNAi design tool
 Sequence analysis

Example of RNAi

DNA for blue

colour gene

Test Plant

Gene is silenced
(no blue colour)
Sequence analysis

RNAi mechanism

DNA
RNAi

mRNA

Protein
X
 Sequence analysis

Off-target prediction

RNAi GCTGCGCATGCTCGAGATGCTGAT

Gene 1 ATCGTAGGCTGCGCATGCTCGAGATGCTGATCTGATGCAGCTGAGTCGGCTGCTTAGGCTCTATCGCT
Gene 2 GCTCGGATGCTGCGCTGAGGTGCTGCGTAGGATTCTGGCTGCGCATGCTCGAGATGCTGATATCTGAT

Barley
genome is
huge, high
chance to hit
more than
one gene!
 Sequence analysis

Design of efficient RNAi constructs

RNAi not efficient RNAi efficient RNAi very efficient

No effect Some blue Blue colour

colour present disappeared
 Sequence analysis

siFi21 Features
Two modes
o Off-target prediction
o RNAi design

Custom database management

Development of a new algorithm for calculating
the RNAi efficiency
Offline support (data confidentiality)
 Sequence analysis

siFi21 Screenshots

http://www.snowformatics.com/si-fi.html
 Analysis of results

Anno
An image browser for manual annotation of
cells
 Analysis of results

Automated microscopic system

Microphenomics
Analysis of results

Image analysis

Image browser for

easy
manual annotation
by mouse or
keyboard.

Up to 10.000 images
per week!
Wouldnt it be
dreamy

to have a light application

and plotting framework
to create and deploy cross-
platform in one go
to revert the ratio of 80% [GUI
development & deployment
time] to 20% [coding time]
 Thank you!

Financial aid Community

Dr. Patrick Schweizer

Dr. Dimitar Douchkov
How we bring RNAi into
the plant?
Gene gun RNAi Reporter to visualize cells

DNA

Shooting

Plants
 Asexual life cycle of powdery mildew
Day 0 Day 1

Day 7 Day 2

Day 3-5
http://www.phytomedizin.org/fileadmin/alte_Webseiten/dokumente/Fachinfo.pdf
Primer Factory
http://www.snowformatics.com/primer-
factory.html

A primer design and primer search tool

 First some theory
The polymerase
chain reaction (PCR)
is a technique used
in molecular biology
to amplify a single
copy or a few copies
of a piece of DNA
across several
orders of
magnitude,
generating
thousands to
millions of copies of
A primer is a short strand of RNA or DNA a particular DNA
that serves as a starting point for PCR. sequence.
 Primer Factory Features
Easily several hundred PCRs per day
Search for Primers in a database to avoid primer
redundancy and reordering (5-10 per primer)
Design Primers (eprimer3 based)
Single or batch mode
Calculate optimal annelaing temperature