Simplicity – Enabling a Rapid Route to Publication
This workshop will focus on a new software platform that allows users to move rapidly from raw data to publication.
The goal of the workshop is to show users that the research ‘story’ is in the data itself waiting to be uncovered and that advanced bioinformatics tools can be configured to rapidly and easily unveil this knowledge. Participants will be invited to provide access to their sequence data during the workshop so that they can use the tool and judge for themselves how science can be accelerated.
It will also provide an informal and vibrant forum for researchers and industry practitioners alike, to share their research results and practical development and provide feedback on how great science can be achieved.
The workshop will have the following agenda:
1. Introduction – publishing with bioinformatics.
2. Grand Challenges in bioinformatics – Speed, Simplicity, Security, Scalability
3. Demonstration of Prokaryote de novo assembly with annotation pipeline will use the following type tools:
Reads quality check (Fastqc)
Trim Adapter and poor quality reads
De novo assembly
SNPs and INDEL analysis
Rapid genome Identification with search of MLST database (Multi locus sequence typing)
Similarity search in databases; Uniprot Trembl, Cath, Pfam and Virulence factors
Multiple alignment for identified rRNA ORFs
Phylogenetic tree construction for identified rRNA ORFs
Codon and amino acid usage charts
4. Rapid Reporting
5. Discussion of Results
6. Hands on Research
Sample sequences will be provided to participants. Participants are also encouraged to provide their own data and on registration will be provided with a secure link where their sequences can be uploaded. Sequences from Base space may also be accommodated. Please note that all sequences submitted will be treated in confidence and participants will retain ownership.
Papers should be formatted according to IEEE Computer Society Proceedings Manuscript Formatting Guidelines (8-page limit, 2-column format).The papers can be submmited online via https://wi-lab.com/cyberchair/2014/bibm14/scripts/ws_submit.php.
The workshop proceeding will be made available online. Selected extended papers from the workshop will be invited for consideration for publication in a special issue of International Journal of Data Mining and Bioinformatics (SCI indexed) .
Sept 10, 2014: Due date for full workshop papers submission
Sept 30, 2014: Notification of paper acceptance to authors
Oct 10, 2014: Camera-ready of accepted papers
Nov 2-5, 2014: Workshops
Dr Paul Walsh, CTO, NSilico Life Science, Cork Ireland, firstname.lastname@example.org
Program Committee Members (tentative):
Paul Walsh, NSilico Life Science
Roy Sleator, Cork Institute of Technology
Elaine Kenny, Trinity College Dublin
Brian Kelly, University College Dublin
Jane Zheng, University of Ulster