A new download of
2014-08-25 ) is now available (svn r466). See the SLiMSuite blog for more details.
Tuesday 26 August 2014
Monday 11 August 2014
A couple of years ago, I made a UPGMA walkthrough for an undergrad course. The slides were available on request but can now be found on GOBLET (the Global Organisation for Bioinformatics Learning, Education & Training website).
Tuesday 5 August 2014
Vicky Schneider BABS seminar this friday - My journey through biology and bioinformatics: my family and other animals
Following InCoB2014, we are lucky enough to be hosting Dr Vicky Schneider to discuss bioinformatics training. As part of her visit, Vicky will be giving a special BABS Seminar this Friday (8 Aug) at 3pm.
The seminar will be followed by “Happy Hour” at 4pm in the Wilton Room 113, Samuels building, UNSW. All welcome!
My journey through biology and bioinformatics: my family and other animals
Speaker: Dr Vicky Schneider
Affiliation: The Genome Analysis Centre (TGAC), Norwich, UK
Abstract: From my roots and growing passion for nature an biology, I will share with you my career pathway and the progression that brought me from an evolutionary field biologists to bioinformatics and a passion for building communities, working and engaging with others to achieve goals, share experiences and best practice in bioinformatics. More than ever, in the era of Next Generation Sequencing and OMICs we need to proactively create the opportunities and activities towards bridging the gap between biologists and computational researchers. Similarly, best practice in programming, storing, annotating and sharing data are crucial towards reproducibility and open science. I will also give you an overview of The Genome Analysis Centre (TGAC), in Norwich, UK where I am currently a member of its Senior Management team and lead the 361° Division on Scientific Training, Education and Learning.
Biography: Before her current post at TGAC, Vicky was the European Bioinformatics Institute (EMBL-EBI) User Training Coordinator. Prior to joining EMBL-EBI in 2007 she held an Assistant Professor position at the University of Bern and the Institute for Aquatic Sciences (EAWAG) and postdocs at the University of Zurich and University of Rome (Torvergata). She studied biology at the University of Rome and obtained her PhD on the evolution of sex at the University of Leiden (NL) and Lyon (France). Vicky played a key role in the creation and establishment of the Bioinformatics Training Network (BTN) which has now evolved into the Global Organisation for Bioinformatics Learning, Education & Training (GOBLET). For more information, see: http://www.tgac.ac.uk/training-outreach/vicky-schneider/.
InCoB 2014: Computational prediction of molecular mimicry in host-pathogen protein-protein interactions
Ranjeeta Menon, Nicolas Palopoli & Richard J. Edwards. F1000Research 2014, 5:1027 (poster)
Many viruses hijack important cellular machinery of their hosts through the convergent evolution of host short linear motifs (SLiMs). We are combining host-pathogen and host-host protein-protein interaction data to explore such “molecular mimicry” across a broad range of human viruses. Computational tools from the SLiMSuite package are being used to assess the potential for bioinformatic analysis of high-throughput experiments to identify novel cases of molecular mimicry.
Monday 4 August 2014
UNSW School of Biotechnology and Biomolecular Sciences is offering a number of Summer Vacation Research Scholarships (SVRS):
Are you a science student who would like the opportunity to experience the real world of scientific research first-hand? Students in the penultimate (second last) year of their undergraduate program in Science or a related discipline are invited to apply for a SVRS to join a BABS research team and participate in research over the coming summer.
Each scholarship is valued at $3,800 and students will participate in a 6-week research project.
The School facilitates collaborative research efforts across discipline boundaries for fundamental discoveries, generation of commercial opportunities and clinical research. BABS has key strengths in environmental microbiology, genetics and cellular biology, molecular medicine, and associated technology development in the areas of functional genomics and many facets of biotechnology. The School has a unique strength in combining fundamental biological and biomolecular sciences with a strong applied biotechnology and medical focus.
See the BABS undergraduate scholarships page for further details and a full list of projects available. We have one advertised project (below) but I am happy to discuss other projects related to any area of research in the lab.
Project: Molecular mimicry in host-pathogen interactions
Many viruses hijack host cellular machinery through the molecular mimicry of host Short Linear Motifs (SLiMs). It is likely that pathogenic bacteria may employ similar strategies. This project will apply state-of-the-art SLiM prediction tools developed in our lab to published datasets of host-pathogen protein-protein interactions. This will help us understand how pathogens mess with their hosts - and how to stop them!
Time project is available: From Early December 2014 to Mid February 2015
Preferred students: Students should have an interest in molecular mechanisms and bioinformatics. Prior experience or an interest in programming would be beneficial but is not required.
Other conditions: This project is computational.
Sunday 3 August 2014
In line with the general retirement of
SeqSuite in favour of bundling everything together in
SLiMSuite, the old @seqsuite twitter account is also being retired. In its place is a new Edwards Lab account with the twitter handle @slimsuite. The tweeting remit will also be broadened to include a variety of lab-related activities, not just SLiMSuite-related matters.