We announce our holiday discount! www.genexplain.com In the period between December 1st 2011 and January 15th 2012, we offer 50% off on the following products: the geneXplain platform, user-friendly, unified online access to a broad range of computational tools. Public domain, commercial or your own tools can be combined to workflows, and standard tasks have been implemented in pre-defined workflows; IMC (In silico Molecular Cloning) and GT (Genome Traveler), handling, interpreting and visualizing your high-throughput and next generation sequencing (NGS) data; PASS (Prediction Activity Spectra for Substances) and PharmaExpert, efficiently assess biological activities of organic drug-like compounds. Get your free trial or demo versions now, try them, and order your licenses during the discount period!

1. Holiday discount, 50% off!
December 1st 2011 - January 15th 2012
We announce our holiday discount!
In the period between December 1st 2011 and January 15th 2012 we offer 50% off on
the following products.
Get your free trial or demo versions now, try them, and order your licenses during the
discount period!
geneXplain Platform
The geneXplain platform is an online toolbox and workflow management system for scientists in the
field of molecular biology. Here, you can store and analyze your experimental data - including
transcriptomics, proteomics, and ChIP-Seq -, search for master regulator molecules, perform gene set
enrichment analysis, and even add your own workflows and scripts.
Key features of the platform:
 Collection, storage and analysis of experimental data
 Loading raw microarray data, BED files and more
 Statistical processing of raw data
 Comfortable work with tabulated data: comparison, joining, subtracting, sorting, etc.
 Mapping to Gene Ontology terms, Gene Set Enrichment Analysis
 Network clustering and search for master regulator molecules, visualization of pathway
diagrams in several different layouts, export in a number of formats
 Dynamic simulations
 Browsing through several databases
 Possibility to graphically program a specific pipeline (workflow), and add new scripts
The geneXplain platform combines a growing number of analytical modules (bricks) under a
standardized interface, which can be flexibly combined to comprehensive workflows via a simple drag-
and-drop system. Predefined workflows are already available, as well as state-of-the-art bricks. Also,
the scientific community is invited to add their own bricks as scripts or plug-ins into the platform.
A fully functional free trial account, as well as further information, is available on our homepage:
http://www.genexplain.com/genexplain-platform

2. IMC
In-silico molecular cloning (IMC) is a renowned software package for comprehensive analysis,
annotation and visualization of genomic features. It has been on the Japanese market for over six
years and is now being distributed internationally.
Key features of IMC:
 Drawing of plasmid maps
 DNA digestion by restriction enzymes
 Ligation of sequences
 PCR, from primer design to gel electrophoresis of the results
 Amino acid profile analysis
 Automatic or manual annotation of features
 Search for homologies, patterns and repeats
 Array analysis
The IMC software package provides a rich functionality; methods from in silico molecular cloning to
genome to array analysis are included in the IMC Array edition (IMC-AE). The IMC Genomics edition
(IMC-GE) focuses on functions to handle genome data, the standard edition (IMC-SE) provides all basic
functions to visualize genomic annotation.
The software runs on Windows, Mac and Linux and has been developed by in silico biology, Inc., in
Yokohama, Japan (http://www.insilicobiology.jp/en).
A free fully functional trial version, as well as further information, is available on our homepage:
http://www.genexplain.com/imc

3. GenomeTraveler
GenomeTraveler (GT) is a comprehensive software package for the analysis of whole genomes, which
supports mapping of NGS fragments, mutation analysis, feature annotation and more.
Key features of GenomeTraveler:
 Mapping of single- and paired-end fragments
 Contig mapping
 de novo assembly
 Import of mapping/assembling results from SAMtool, SOLiD, Velvet and Phrab
 Profile peak detection
 Mutation and SNP analysis
 Expression analysis
 The alignment viewer includes: search, annotation and comparative genome functions
GenomeTraveler is a program for next generation sequencing data analysis and annotation. It can
handle data from Roche/454 GS FLX, ABI SOLiD and Illumina GA, and provides a graphical interface
for smooth viewing and editing of mapping and assembly results.
The software runs on Windows, Mac and Linux and has been developed by in silico biology, Inc., in
Yokohama, Japan (http://www.insilicobiology.jp/en).
A free fully functional trial version, as well as further information, is available on our homepage:
http://www.genexplain.com/genome-traveler

4. PASS
The acronym PASS stands for Prediction of Activity Spectra for Substances. After entering structural
formulas of drug-like organic compounds - either a single structure or a big library - the program
instantly gives a list of predicted bioactivities, accompanied by estimated mathematical probabilities.
Key features of PASS:
 Standard MOL and SDF files are used as input structural data
 Multilevel Neighborhood of Atoms (MNA) descriptors are used to create robust and predictive
SAR models
 Activity spectra for thousands of compounds can be predicted within minutes
 Impact of each atom on a particular activity is highlighted by its color
 Currently, over 4,300 bioactivities can be predicted
 Mathematical algorithm based on Bayesian estimates of probabilities
PASS can quickly predict biological activity spectra for organic drug-like compounds qualitatively. The
activities that can be predicted range from pharmacotherapeutic effects, biochemical mechanisms and
toxic and adverse effects to influence on the metabolism, gene regulation and transporter-related
activities. The software runs under Windows.
Since more than 15 years, PASS is permanently being developed by Vladimir Poroikov, Dmitry
Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of
Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow
(http://www.pharmaexpert.ru/PASSOnline/).
A free demo version, as well as further information, is available on our website:
http://www.genexplain.com/pass

5. PharmaExpert
PharmaExpert analyzes the relationships between biological activities, drug-drug interactions and the
multiple targeting actions of chemical compounds. As a pharmacological knowledge-based tool, it
provides in silico screening of compounds using PASS prediction results.
Key features of PharmaExpert:
 Mechanism-effect relationship (MER) base, manually curated by experts, containing 11,049
mechanism-effect relationships
 Selection of compounds with required therapeutic but without side effects
 Comparative analysis of compounds with similar structures
 Selection of compounds with multiple mechanisms of action
 Analysis of drug-drug interactions with regard to their pharmacokinetic, pharmacodynamic and
adverse effects
PharmaExpert uses PASS (Prediction of Activity Spectra for Substances) predictions as input
information. It provides a comfortable solution for data mining of the PASS prediction results to find
the best drug-like candidates from a set of compounds. The core of the program is a mechanism-effect
relationship (MER) base, which is used to determine cause-effect relationships for the compounds. Like
PASS, the software runs under Windows.
Since more than 15 years, PharmaExpert is permanently being developed by Vladimir Poroikov, Dmitry
Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of
Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow
(http://www.pharmaexpert.ru/PASSOnline/).
A free demo version, as well as further information, is available on our homepage:
http://www.genexplain.com/pharmaexpert

6. About geneXplain GmbH
GeneXplain GmbH has been founded in April 2010 and is based in Wolfenbüttel, Germany. The
company aims at providing a comprehensive set of computational tools supporting the complete drug
development pipeline from the statistical evaluation of high-throughput data, their biological
interpretation, and identification of potential targets to the prediction of most promising lead
structures. The geneXplain platform is based on BioUML and has been developed together with the
Institute of Systems Biology, Novosibirsk, Russia, where this leading-edge technology originates.
Your geneXplain team
geneXplain GmbH
Am Exer 10b
D-38302 Wolfenbüttel
Germany
phone: +49-5331-9450434
e-mail: info@genexplain.com
URL: http://www.genexplain.com
Facebook: http://www.facebook.com/genexplain
Twitter: https://twitter.com/#!/geneXplain
LinkedIn: http://www.linkedin.com/company/genexplain
Google+: https://plus.google.com/104816244332282237960