A further Six samples were isolated and sent for sequencing to Eldabiotech and the data has returned showing good quality data.  Nsilico have already started the assembly, annotation and generating draft genome announcements with Simplicity™.  Below is an image of the quality taken from the Illumina Basespace website.

Following the assembly and annotation of 8 samples, six genome announcements were accepted in the Genome Announcements (genomeA) journal at http://genomea.asm.org/

The announcements were for samples:

• Staphylococcus aureus 
  

• Enterococcus faecalis 
  

• Pantoea sp. 
  

• Staphylococcus warneri 
  

• Serratia marcescens 
  

• Streptococcus agalactiae 
  

The announcements can be found here: http://genomea.asm.org/search?submit=yes&submit=Submit&pubdate_year=2014&volume=&firstpage=&doi=&author1=Walsh&author2=&title=&andorexacttitle=and&titleabstract=&andorexacttitleabs=and&fulltext=&andorexactfulltext=and&fmonth=&fyear=&tmonth=&tyear=&journalcode=ga&tocsectionid=all&format=standard&hits=10&sortspec=relevance&submit=yes

The rise in antibiotic resistance is leading to a growing number of deaths from sepsis, experts warn.  

Deaths from sepsis are on the rise due to growing antibiotic resistance which means previously harmless infections can become fatal, a healthcare expert has warned.  Mark Bellamy, president of the Intensive Care Society, said new antibiotics must be developed to prevent the spread of resistant bugs which can lead to sepsis.

The full story can be read here:
http://www.telegraph.co.uk/health/11047019/Sepsis-is-on-the-rise-warns-medical-expert.html

Nsilico and CIT, two members of the ClouDx-i project will present their progress with the Marie Curie funded project at the 4th Irish Next-Generation Sequencing Meeting held at Trinity Biomedical Sciences Institute on the 13th of June.


The 4th Irish Next-Generation Sequencing Meeting will consist of a diverse set of talks on different applications of next generation sequencing technology. Please see the programme below for more information. 

The sequencing of the 10 samples for the Cloudxi project has completed.  The 10 samples were submitted for Mate-Pair library prep and 2x300bp sequencing and are now available for download from basespace for analysis.

The bioinformaticians now must analysis the huge quantity of data produced by the 10 samples.  Below is a list of the samples and sequencing information.  

The graph below shows the quality of data produced.

Nsilico and some of the ClouDx-i team will be attending and participating at the Conference on Bioinformatics and Biomedicine (BIBM) in July this year.  Nsilico's Paul Walsh is on the Industry Program Committee.

http://scm.ulster.ac.uk/~bibm/2014/index.html

The Conference has established itself as the premier research conference in bioinformatics and biomedicine. IEEE BIBM 2014 provides a leading forum for disseminating the latest research in bioinformatics and health informatics. It brings together academic and industrial scientists from computer science, biology, chemistry, medicine, mathematics and statistics.

ClouDx-I researchers published an article entitled “Big data, Hadoop and cloud computing in genomics” in the Journal of Biomedical informatics in July 2013.  http://www.sciencedirect.com/science/article/pii/S1532046413001007

Since then this article has been viewed 4960 times and is the fourth most downloaded article in this journal in the last 90 days (March 2014).


Below is the article dashboard showing details.

The biologists in the ClouDx-i team have extracted DNA from 11 samples.  10 samples were suitable for sequencing and one sample was degraded.  Nsilico have sent the good samples to EldaBiotech in Dublin for sequencing with results due sometime in April.

The samples were from the following species:

1. Strep agalactiae Group B
   
2. Enterococcus faecalis
   
3. Escherichia coli
   
4. Pantoea species
   
5. Staphylococcus aureus
   
6. Enterococcus faecalis
   
7. Staphylococcus aureus
   
8. Serratia marcescens
   

Synthetic biotech is evolutionizing and becoming an integral part of every major industry, including medicine, energy, agriculture and manufacturing.
http://synbioaxlr8r.com/future/

Paul joined some of the top experts in Synthetic Biology in one of Europes top biotech hubs, to meet and discuss that exciting future, as well as the steps and hurdles todays SynBio entrepreneurs, investors and researchers must face to get there.

 Dr Walsh presented progress on ClouDx-i and also sat on a panel for discussion and raised issues about the future of computational biology in clinical settings.