PWS.pdf

Performance Work Statement for server administration and bioinformatics consulting

Description of the work to be performed

Server and software administration

Remote software administration of two AMD 64-core, 512GB RAM Dell PowerEdge servers residing at the SEPRL facilities. This includes management of all software and users at and above the level of the operating system. Installation and maintenance of the Debian GNU/Linux operating system, including monitoring and patching of security vulnerabilities and non-critical system and software updates and monitoring of system health and performance via rsyslog logging and automatic notifications.

• Maintenance of the server-based authentication and security configurations. Users will access and interact with the systems through ssh and Galaxy (over HTTPS). Management of machined-based iptables rules to allow access only through the ports needed for these routes of access and only from local IP addresses.

• Installation and maintenance of a local Galaxy instance (http://galaxyproject.org), including user management and maintenance of local data sources and pipelines as requested by SEPRL users.

• Installation, updating, and troubleshooting of command-line software tools for sequence assembly and bioinformatic analysis. This includes assembly software for traditional, second- and third-generation genomic and transcriptomic sequencing data (e.g. mira, SOAPdenovo2, sga, velvet, Trinity, etc) and other common tools for data QC, manipulation, and analysis (e.g. FastQC, cutadapt, samtools, Picard, bedtools, R/Bioconductor, etc). Initial server setup will include installation of a standard tool set.

Software installation will be coordinated with the local IT department to ensure compliance with USDA/ARS IT protocols and practices.

• Management of raw sequencing data and shared databases (e.g. blast, bwa and bowtie2 databases/pre-built indices), including coordination with sequencing facilities for data transfer.

• Testing of a system for clustering/distributed resource management (e.g. MPI + Torque/Maui) frame to facilitate resource sharing between the two machines.

• Subsequent to setup of the servers, an initial two-day site visit to finalize arrangements and to provide introductory instruction to potential users on access and use of the machines.

• Training and support to SEPRL employees on aspects of their work related to use of the servers, sequence assembly and bioinformatic analysis. Support will be provided via e-mail and phone communication (aside from an initial site visit to provide hands-on training in server use). Examples of such support include (but are not limited to):

o General instruction and support on using and navigating the server command-line and Galaxy interfaces.

http://galaxyproject.org/ o Advice on experimental design (sequencing platform, read depth, etc) for sequencing-related projects.

o Q&A and troubleshooting on software use and best practices as requested by users.

o Support and advice on data exploration and analysis pipeline design for specific projects (e.g. initial quality control and exploratory analysis, pre-processing, choice of assembler and assembly parameters, etc).

o Advice on data visualization, including instruction on the use of R to visualize data and prepare publication-quality visualizations. Provide custom code for data visualization and figure preparation needs not met by existing software tools.

Assembly and analysis performed

In addition to providing training and support to SEPRL scientists the contractor will perform assembly, data analysis and coding on its own for projects led by SEPRL scientists. Examples of such tasks may include (but are not limited to):

• assembly and in silico finishing of viral and bacterial genomic and transcriptomic sequencing data from traditional, second- and third-generation platforms

• data analysis for genomic variant detection (SNP, indel, SV) and RNA-Seq or microarray-based differential expression analyses using R/Bioconductor

• authoring of custom tools in Perl for analysis tasks not covered by existing software

• Preparation of publication-quality figures using R

Location of Work

The Southeast Poultry Research Laboratory, 934 College Station, Athens, GA, USA

Period of Perfomance

The base period of performance will be December 15, 2014-December 14, 2015.

Option Year 1 - December 15, 2015-December 14, 2016 Option Year 2 - December 15, 2016-December 14, 2017 Option Year 3 - December 15, 2017-December 14, 2018 Option Year 4 - December 15, 2018-December 14, 2019

Deliverable schedule

Contractor will respond to most e-mail requests for support within four business days (typically within one day for simple questions/requests).

Expected timelines for assembly and analysis work performed will be discussed prior to commencement of the work. It is expected that most smaller projects will take between two weeks and one month for completion of the initial work. The primary mode of communication between with SEPRL will be via e-mail and the secondary mode of communication will be by phone.

Performance will include up to 20 hours per month of support and in-house work as described above. An anticipated distribution of these duties is as follows:

Task Hours/month Server administration/maintenance 6 Assembly/analysis (support for SEPRL employees)

Assembly/analysis 6

If less than 20 hours of support are needed in a given month, the remaining balance can be carried over up to one month in the future. Therefore, the maximum number of regular billable hours available under this agreement will be 40 hours/month. Time will be charged against carry-over hours first and regular current-month hours second. Hours will not be carried over to subsequent yearly renewals of the contract (if any).

Applicable performance standards

Contractor will agree not to share with any third party, or use for any purpose beyond the scope of its work with SEPRL, any data or information provided by SEPRL (directly or indirectly) which is not already in the public domain, without prior consent from the client. Contractor will agree not to share with any third party, or use for any purpose beyond the scope of this Project, any information or data generated during the course of the partnership and derived directly or indirectly from information provided by the client not already in the public domain, without prior consent from the client.

Special requirements

Knowledge of Newcastle disease virus, chicken viruses, and chicken genome is required.