Open Access Highly Accessed Software

Applications of the pipeline environment for visual informatics and genomics computations

Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman and Arthur W Toga*

BMC Bioinformatics 2011, 12:304  doi:10.1186/1471-2105-12-304

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Errors in Table 1. Comparison of common graphical workflow environments

Scott Markel   (2013-01-11 12:35)  Accelrys email

Thank you for including Pipeline Pilot in your review.

I would like to address a few errors in Table 1 regarding our product.

1. We don't require third-party tools to be recompiled. We use a wrapper approach similar to LONI and call these command-line executables directly, as is.

2. While we do have mechanisms for storing small amounts of data internally, the NGS collection uses standard file formats for reference sequences (FASTA), mapped reads (BAM), and features (GFF3, VCF). We only use the internal storage mechanisms for temporary variables and data, not for user data.

3. Pipeline Pilot, now the Accelrys Enterprise Platform, is platform independent, running on both Windows and Linux. The NGS collection is Linux, 64-bit only.

4. We do have a client-server model. Pipeline Pilot is the Windows-only client and the Accelrys Enterprise Platform is the Windows/Linux server.

5. The Accelrys Enterprise Platform is grid- and cluster-enabled. We support Oracle Grid Engine (OGE), PBS Professional, Platform LSF, and custom grid engines.

Competing interests

I'm the software architect for Next Gen Sequencing collection for the Accelrys Enterprise Platform (Pipeline Pilot).


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