Dear all
The Luxembourg Centre for Systems Biomedicine (LCSB) at the University of Luxembourg is seeking an enthusiastic team member for the following position:
System administrator for ELIXIR Node in Luxembourg (m/f)
* Initial contract duration : 3 years, 40h/week, extension possible
* Employee status (start date: as soon as possible)
* Ref. : S-STR-4029-00-B
The Luxembourg Centre for Systems Biomedicine (LCSB) is an interdisciplinary research centre at the University of Luxembourg. LCSB develops and applies systems-level approaches to gain insight into the molecular and cellular mechanisms of human diseases. Experimental and computational approaches are combined to analyse the complexity of biological systems underlying disease pathogenesis. The LCSB is pioneering the way for a predictive, preventive and personalised medicine. LCSB is currently establishing the ELIXIR (the European life-sciences Infrastructure for biological Information www.elixir-europe.org<http://www.elixir-europe.org>) national node of Luxembourg focusing on “Clinical and Translational Medicine Research Informatics”.
We are looking for a System administrator for the prospective ELIXIR Node. The job owner will help to provide a secure, scalable and highly available Virtual Private Cloud (VPC) & IT environment adequate to the needs of the ELIXIR services and user community, through proactive monitoring and support of the heterogeneous hardware and software components. One important task will include the support of the whole scientific software landscape but will also include the further development and refinement of existing and upcoming software analysis pipelines. The job owner should be able to perform and lead data management / processing tasks.
Your Role
Duties of the position include, but are not limited to:
* Perform daily duties as regards VPC configuration management, on as-needed basis
* Build Inventory of VPC Equipment; Hardware, Software, Services and redundancy Procedures
* Maintain and monitor support information in Ticketing System(s) and related tools
* Provide system and network administration and support firewalls, network organisation, and be able to handle storage services, including fileserver-client issues
* Write and maintain documentation for technical procedures, on as needed basis
* Improve on procedures/practices, as advancements in the field dictate
* Become the primary administrator for outsourced services/accounts (e.g. web hosting) and assist in the procurement of in-house services via external vendors, if/when so desired
* Assist with system backup and recovery services and system administration tools and processes, e.g. user administration, networking, file servers; familiarity with the LAMP stack, TCP/IP networking and supporting them in tandem
* Provide support for bioinformatics tools and software pipelines and be involved in their further development and refinement
* Be responsible to lead bioinformatics related data analysis tasks
Your Profile
* Degree in computer science or bioinformatics or related fields.
* Strong system administration and hardware experience including full stack up to OS virtualization is required (OpenStack / oVirt knowledge will be considered an asset).
* Good computer programming experience (Python, linux scripting)
* Experience with Puppet, Ansible or Chef will be considered an asset
* Knowledge of modern web development technologies will be considered an asset
* Excellent communication skills and the ability to articulate clearly the scientific and technical needs and to work within an interdisciplinary setting, communicating with other internal/external partners.
We offer
* A fully funded position with a very competitive salary.
* Participate in the building of state-of-the-art translational medicine platform to support clinical projects from national, EU and beyond.
* An opportunity to join the fast-growing Bioinformatics Core Facility group headed by Dr. Reinhard Schneider in the newly created LCSB.
* An exciting international environment.
The University is an equal opportunity employer.
Further Information
For questions, please contact Venkata Satagopam (venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu>).
Applications (in English) should contain the following documents:
* A detailed curriculum vitae
* Cover letter mentioning the reference number
* List of publications/infrastructure and software projects
* Description of past experience and future interests
* Name and addresses of three referees
Please apply online until 10th June 2016.
URL: http://emea3.mrted.ly/11opj
--
Venkata P. Satagopam
Bioinformatics Core
Luxembourg Centre For Systems Biomedicine (LCSB)
University of Luxembourg
Campus Belval, House of Biomedicine II
6, avenue du Swing
L-4367 Belvaux
T +352-466-644-6421
F +352-466-644-6949
venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu>
http://lcsb.uni.lu
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****CALL FOR PAPERS******
15th International Workshop on Data Mining in Bioinformatics (BIOKDD'16)
August 14 2016
San Francisco, USA
http://home.biokdd.org/biokdd16/http://www.facebook.com/Biokdd
The goal of the 16th International Workshop on Data Mining in Bioinformatics (BIOKDD'16) is to encourage KDD researchers to tackle the numerous challenges of mining and learning in Bioinformatics, Biomedical and Health Informatics. Thus this year, the workshop will feature the theme of “Latest Advances of Mining and Learning in Bioinformatics, Biomedical and Health Informatics”. This field focuses on the use of data mining and machine learning approaches for the analysis of the large amount of heterogeneous complex biological and medical data being generated together with innovative applications in biomedical and health informatics. The key goal is thus to build accurate predictive or descriptive models from data enabling either novel discoveries in basic biology and medicine or an effective use of the latest advances of data mining in healthcare.
We encourage papers that propose novel data mining techniques for areas including but not limited to
* Predictive modeling for complex phenotypes from large-scale biological data
* Discovery of biological networks and pathways underlying biological processes and diseases
* Processing of new/next-generation sequencing (NGS) data
* Discovery of genotype-phenotype associations
* Biomarker discovery in clinical and genomic data
* Data analytics for clinical informatics
* Data integration for biomedical applications
* Comparative genomics
* Metagenome analysis using sequencing data
* RNA-seq and microarray-based gene expression analysis
* Genome-wide analysis of non-coding RNAs
* Genome-wide regulatory motif discovery
* Structural bioinformatics
* Correlating NGS with proteomics data analysis
* Functional annotation of genes and proteins
* Cheminformatics
* Special biological data management techniques
* Information visualization and Visual analytics for biomedical data
* Predictive modeling for personalized treatment
* Semantic web and ontology in Biomedicine
* Privacy and security issues in genomics and healthcare
* Text mining for biomedical literature and clinical notes
* Information retrieval for healthcare and Biomedical applications
* Biomedical signal analysis and processing
* Intelligent medical data management
* Collaboration technologies for biomedicine
* Social networks for biomedicine
**Important Dates**
May 27th, 2016 Deadline for Submission of Papers
June 13th, 2016 Notification of Acceptance; Workshop Registration Open
June 30th, 2016 Submission of Camera-ready Papers
August 14th, 2016 Workshop Presentation
All deadlines are at 11:59 PM Pacific Standard Time.
**Submissions**
Papers should be at most 10 pages long, single-spaced, in font size 10 or larger with one-inch margins on all sides. Using the ACM Proceedings Format is highly recommended. Paper should be submitted in PDF format through EasyChair at the following link: https://easychair.org/conferences/?conf=biokdd2016
Papers will be published in the webpage. A selection of accepted papers will also be invited to be submitted to a special issue of the reputed IEEE Transactions on Computational Biology and Bioinformatics.
**Workshop Organizers**
Program Chairs:
Sara C. Madeira, Instituto Superior Técnico, <sara.madeira(a)tecnico.ulisboa.pt>
Chandan K. Reddy, Wayne State University, USA <reddy(a)cs.wayne.edu>
General Chairs:
Mohammed J. Zaki, Rensselaer Polytechnic Institute, <zaki(a)cs.rpi.edu>
Jake Y. Chen, Indiana University - Purdue University Indianapolis, <jakechen(a)iupui.edu>
Dear all,
We are looking for a PhD candidate in bioinformatics at the Delft
Bioinformatics Lab at TU Delft, The Netherlands, to work on a project
looking to develop rapid diagnosis of drug resistant and mixed TB
infections.
Project and application details below.
best,
Thomas
*
PhD-position in Computational Microbiology*
*Title
*Rapid diagnosis of drug resistant TB infections//
*Project leader*
Thomas Abeel
Delft Bioinformatics Lab – Pattern Recognition and Bioinformatics –
Department of Intelligent Systems
Faculty of EEMCS, Delft University of Technology (TU Delft)*
*
*Job description*
Despite treatment options, TB is killing 1.5 million people each year,
the vast majority in developing nations. Current diagnostics often take
several weeks or months, which is too long to save the lives of the
patients or to prevent further transmission. This project collaborates
with Dr. Pym of the K-RITH research institute in Durban South-Africa to
develop an innovative rapid diagnostic that accurately identifies
currently undiagnosable TB infections, i.e. mixed and drug resistant
infections. This will be done by computationally identifying markers
that are indicative of these infections in genomic data which are then
used to design the diagnostic using existing sequencing technology.
Your objectives in this project are to identify novel drug-resistance
conferring mutations, to create a predictive model for drug resistance
and mixed infections in TB and to explore the options to turn these
insights into a prototype point-of-care molecular diagnostic. We have a
collection of sequencing and meta-data from >8000 diverse TB strains. We
now have the unique opportunity to leverage these data to make a global
societal impact. You will integrate public and private data sets to
associate mutations with phenotypes, such as drug resistance, with
state-of-the-art computational approaches.
*Requirements*
The ideal candidate has an Msc degree in bioinformatics or alternatively
a degree in computer science or (micro-)biology with strong affinity or
experience in the complementary field. He/she must be able to work
effectively in a multidisciplinary team. The candidate shares our view
that communication skills are important, as is the ability to interact
with peers, students and technical staff. //
-Programming, algorithm development and scripting experience are desirable
-Wet-lab experience is a plus
-Experience in microbial genomics is a plus
//
*Information and application*
For more information about this position, please contact Dr. T. Abeel
(t.abeel(a)tudelft.nl <mailto:t.abeel@tudelft.nl>). To apply, please
e-mail a detailed CV (including grades and English certification if
applicable), cover letter and at least two personal letters of
recommendation. Please submit your full application by June 1, 2016 to
t.abeel(a)tudelft.nl <mailto:t.abeel@tudelft.nl>.More information about
the section: http://bioinformatics.tudelft.nl/and the project leader:
http://www.abeel.be/
*Conditions of employment
*TU Delft offers an attractive benefits package, including a flexible
work week and the option of assembling a customised compensation and
benefits package. Salary and benefits are in accordance with the
Collective Labour Agreement for Dutch Universities.
As a PhD candidate you will be enrolled in the TU Delft Graduate School.
TU Delft Graduate School provides an inspiring research environment; an
excellent team of supervisors, academic staff and a mentor; and a
Doctoral Education Programme aimed at developing your transferable,
discipline-related and research skills. Please visit www.phd.tudelft.nl
for more information.
