The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology

Abstract

Summary: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking.

Availability: Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3.

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Drug2Gene

Drug2Gene is a free knowledge integrated data repository unifying a number of popular public resources to provide structured and organized information for identified and reported relations between genes/proteins and drugs/compounds. It allows user's interactive management by the ability to flag, comment and update relations, to import new drug-gene relations valuable for a specific project. Gene orthology and similarity information is matched to certain relationship entries assisting the prediction of new unreported drug-gene associations. You can go to the original source of the reported relation and explore for more facts, details and evidences. 

website

CloVR

"Background

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.

Results

We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms.

Conclusion

The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing."

http://clovr.org/

MedWorm: a RSS based utility

"MedWorm is a medical RSS feed provider as well as a search engine built on data collected from RSS feeds. RSS stands for Really Simple Syndication and it is a technology used to simply publish and gather details of the very latest information on the internet. You can read more about RSS here.

MedWorm collects updates from over 6000 authoritative data sources (growing each day) via RSS feeds. From the data collected, MedWorm provides new outgoing RSS feeds on various medical categories that you can subscribe to, via the free MedWorm online service, or another RSS reader of your choice, such as Bloglines, Newsgator, Google Reader or FeedDemon.

The best way to get a feel for the information that MedWorm can provide is to have a browse through the various categories on the menu above. New categories are being added all the time and we are happy to receive requests for new ones if you can't find the category of your choice."

Its web address is http://www.medworm.com/.

Legal Disclaimer: This weblog is not affiliated with MedWorm in any way.