All workshops and Tutorials will be held on the 28th of September at the Bielefeld University.


 

CELLmicrocosmos neXt workshop

virtual cell – on the boundary between bioinformatics and chemoinformatics

Sunday, September 28
10am–12pm: Hands-on tutorials, 2pm–6pm: Workshop, detailed program on workshop homepage
Room: U2-205

Abstract

The creation of a virtual cell is a complex interdisciplinary vision which implies the combination of different research fields. Already the creation of microscopic images requires techniques combining biological, chemical as well as physical knowledge. But after the image generation process is finished, the in silico work begins, leading e.g. from a stack of microscopic images to a three-dimensional model. Here, information technology is indispensable. There are numerous approaches to create a cell model at the mesoscopic level. But there are even more aspects, how this model can be enriched with information. Data integration represented by a huge number of databases can be used to acquire information on the functional level, such as biological networks, concentrations, localizations or other publication-based data. On the molecular level, there are many efforts to simulate, analyze and visualize membranes, proteins, vesicles, requiring large computer clusters and very specific chemophysical knowledge. Usually, all these different approaches are not combined, because in silico experiments try to answer very specific questions. But how will it be possible to integrate these different approaches into a virtual cell environment for future scientific and/or educational purposes? Which new developments have to be taken into account? How is it possible to reasonably combine abstract and structural data? And might it be possible to approach synthetic biology with such a system in the future?

To examine these questions and to find out in which way we can join our efforts, we invite contributions from different fields related to Bioinformatics and Chemoinformatics, which fit into the context of structural as well as functional modeling and visualization. Potential topics are:

  • Integrative Bioinformatics
  • Structural Bioinformatics
  • Cell Modeling and Visualization
  • Molecular Modeling and Visualization
  • Membrane and Vesicle Simulation
  • Network Analysis and Visualization
  • Data Integration
  • Microscopic Image Segmentation
  • Biological Interactive Web Visualization
  • Stereoscopic 3D Visualization in Biology
  • Subcellular Localization

Background

A prototype of a static virtual cell environment combining different cytological levels is presented by the CELLmicrocosmos project. Ten years of development, starting from an initial cell animation, leading over a first educational interactive prototype, proceeding with a number of cell modeling projects. Today, approaches have been presented at the molecular, mesoscopic as well as functional level. But instead of funding from large organizations, the driving force behind this project were students. Bachelor, master and diploma students were involved in the development of different modeling tools and 3D models. But what will be the next level? Now, the resulting projects can be used as a starting point for a collaborative project, providing a visual framework to combine and present different levels of cytological knowledge. The future key features of a virtual cell framework have to be defined.

Program Committee

  • Jens Allmer (Izmir)
  • Patrizio Arrigo (Genoa)
  • Marc Baaden (Paris)
  • Wolfgang Brandt (Halle)
  • Ming Chen (Hangzhou)
  • Davide Gadia (Milan)
  • Vladimir Ivanisenko (Novosibirsk)
  • Luis E. Gurrieri (Ottawa)
  • Benjamin Kormeier (Bielefeld)
  • Jens Krüger (Tübingen)
  • Andreas Keller (Saarbrücken)
  • Matthias Lange (Gatersleben)
  • Harald Lanig (Erlangen)
  • Frank Oellien (Ludwigshafen)
  • Ahmet Raşit Öztürk (Ankara)
  • Sebastian E. Schneider (New York)
  • Falk Schreiber (Melbourne)
  • Björn Sommer (Chair, Bielefeld)

Supplementary information: http://neXt.CELLmicrocosmos.org


 

Tutorial: Information Visualization with Omix

Sunday, September 28
10am–6pm
Room: V2-121

Effective integrative visualization solutions bringing together data from experiment and simulation are of central importance to generate insights and new hypotheses. Thus, the interactive network-centric visual analysis of data sets has become an integral part of systems biology investigations.

Omix® is a tool for customizable visualization of multi-omics data in the context of biochemical networks. Omix provides best serving user guidance. Graphical model creation in Omix is supported by automatic graph drawing and semi-automatic network layout techniques tailored to the application field of biochemical network.

Omix allows to visualize data in an unprecedented degree of flexibility. The user can create sophisticated visualizations and animations in quick and easy dialog-based manner. Furthermore, visualization can be created by scripting because Omix allows programmable access to the visual appearance of the diagram components. By this, users can design the data visualization process according to individual requirements.

Multiple plug-ins are available extending Omix with data management, model analysis (FBA, thermodynamics, Flux Modes), database access (KEGG, BioCyc) and modeling features. Kinetic models of biochemical processes can becreated with Omix in graphical manner. Furthermore, Omix is a comprehensive modeling tool for isotope-based metabolic flux analysis.

Omix produces images and videos in widespread file formats. Furthermore, network models can be exported to SBML, SBGN, 13CFLUX2, Matlab, Dymola, and more.

By providing easy access to data visualization and modeling, Omix is well suited as pre- and post-processing framework both, for experimenters and for modelers working interactively together in a rapidly evolving research field of systems biology and life sciences.
The workshop addresses researchers of all disciplines that are interested in information visualization in the context of biochemical networks. In eight hours tutorial course on September 28, you will learn how to create high-qualitative information visualization Omix. Furthermore, an overview is given about the modeling capabilities of Omix. Each participant requires a Laptop for the practical exercises.

The workshop is organized and held by Peter Droste, CEO, Omix Visualization


Supplementary information: www.omix-visualization.com


 

Cloud Computing Tutorial

Sunday, September 28
10am–12pm: AmazonWebServices Introduction (Amazon), 2pm–4pm: Docker Tutorial, BiBiCloud Introduction, BiBiCloud Hands-on, 4.30-5.30pm: Scaling up BiBiCloud Applications
Room: V2-105/121

The need for high-throughput data analysis has grown tremendously since the introduction of next-generation sequencing (NGS) platforms. The massive amount of data produced creates a new class of resource barriers to be overcome including limited bandwidth, storage volume and compute power. Small research labs can hardly cope with the data generated. A solution to the mere resource problem are private or commercially available cloud computing environments as virtually unlimited and flexible resources. However, the problem of making suitable software available on these resources remains to be addressed.

In the first part of the tutorial, representatives from Amazon, Germany, will present the Amazon Web Services (AWS) cloud computing environment and its underlying services like EC2, S3, EMR, etc. (to be confirmed).

In the second part, we will introduce participants into Bielefeld University’s BiBiCloud framework. The BiBiCloud framework aims to support developers in setting up both server environments and tool deployment, as well as transparently integrating cloud resources. We will introduce BiBiCloud’s five central parts:

BiBiServ Framework

BiBiServ is a flexible web application framework with few prerequisites that can be installed on any Unix-like system within minutes. Applications are integrated as so called BiBiApps and can be (un-)deployed during server runtime. The framework supports DRMAA-compatible compute grids for compute intensive applications and has a cloud space junction for transfer of large datasets. The framework supports anonymous usage as well as a private area (MyBiBiServ) for registered users with additional user-specific functionality.

BiBiApp Wizard

Within the BiBiServ framework, each BiBiApp is generated from a central description that contains all information necessary to deploy a tool on the server. From our 16 years’ experience hosting bioinformatics tools, we learned that it is crucial to separate the tool description from the implementation in order to keep up a persistent availability of our tools. The BiBiServ module comes with the BiBiApp Wizard assisting the developer to annotate the tool using a pre-defined ontology in a comfortable way. During a code generation process, a BiBiServ App Project is built from the description as a J2EE project. It allows generating code for different interfaces (web pages, REST and SSWAP services). The BiBiServ framework supports data streaming from and to a cloud storage resource, such as Amazon‘s S3.

InstantBiBi

The InstantBiBi module allows an easy setup of a BiBiServ instance on any Unix-based system. It automatically installs an application server, the BiBiServ framework, BiBiApp Wizard and optional extensions on a local or cloud-based machine. This allows developers to test their BiBiApps before installation on a production system, as well as easily setting up a production system in the cloud.

BiBiGrid Framework

BiBiGrid is a simple to use entry to the Amazon Web Service (AWS) world (see Figure). Instead of moving the data to the applications, we move our server environment and BiBiApps to the data. BiBiGrid supports a flexible and scalable way to obtain cloud based compute resources. BiBiGrid starts predefined Amazon Machine Images (AMIs) for the master and a desired number of compute nodes. Depending on chosen instance types, local discs are used as fast RAID storage for temporary or shared data, such as program binaries and databases. Elastic Block Storage (EBS) volumes can be mounted to the master and each compute node. The BiBiServ framework is set up during master instance initialization and allows web based access to tools, data and analysis results.

BiBiS3

Amazon S3 is a cloud storage service for large amounts of data. Bioinformatic pipelines running on EC2 compute instances need fast access to the data. Our BiBiS3 module provides very efficient and scalable approaches to transfer data both to

and from Amazon S3. The features we implemented are parallel transfer of multiple chunks of data („multipart“ up- and download), recursive transfer of whole directories with parallelization of multiple file downloads, and simultaneous, distributed download via a cluster to either an NFS-shared directory, or split downloads of only smaller chunks of files.

 

KEY DATES

Conference:
September 29 - October 1
Workshops & Tutorials:
September 28

Submission deadline:
June 9 (papers, workshops)

Notification of acceptance:
June 14(workshops)
July 7(papers)

Poster abstract submission:
July 14

Final version due:
July 21

Travel grant applications:
August 10 (read more...)

Early registration deadline:
August 28

PROCEEDINGS

available online...

POSTER AND FLYER

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