PhD position targeting a exciting project in bioinformatics applied to metagenomics and Big Data management and visualization in project ITN BIG4

Organization
Era7 Bioinformatics
Job Location
Plaza de Campo Verde 3
18001 Granada
Spain
Salary
approximate base rate 2,700 € per month
Job Description

TASKS TO BE DEVELOPED BY THE CANDIDATE:

Design, implementation and testing of a cloud based system for the storage and analysis of genomic and metagenomic data and a layer on top of Bio4j for facilitating the use of this platform for systematists working with insects.

Based on the pipelines and Cloud based methods developed by ERA7, the objectives are:

−     To design, develop and test systems for analysis of data for insect metagenomes.

−     To design, implement and test Bio4j queries and a biological solid interface adapted to the knowledge area of systematics.

−     Design, developing and testing of innovative and interactive visualization tools for biological Big Data

 

 

General information and guidelines for applications.

This position is available at Era7 Bioinformatics (https://era7bioinformatics.com), a research intensive SME focused in Next Generation Sequencing projects.

The selected candidate will be based in Era7 Bioinformatics facilities at Granada, Spain and will be part of the international cross-disciplinary training consortium BIG4: ‘Biosystematics, Informatics and Genomics of the 4 big insect groups’ funded by the European Union Marie Skłodowska-Curie Innovative Training Network Program (for details about BIG4 see Page 6).

The Position is for 3 years with very competitive salary (approximate base rate 2,700 € per month), additional family allowance for married students, and sufficient research funds.

 

We seek highly motivated applicants from any country of the world.

Due to the requirements of the Marie Skłodowska-Curie Program applicants should not hold PhD degree and, at the time of enrolment in the PhD program in Granada (Spain), should have less than 4 years of research experience (counted as time of employment in research since receiving a degree allowing enrolment in the PhD program). Additionally, at the time of recruitment, applicants must not have resided or carried out his/her main activity (work, studies, etc.) in Spain for more than 12 months in the 3 years before his/her recruitment for the PhD project.

Requirements

Apart from general skills and attitudes for doing high level research and working in a friendly and encouraging environment, special skills for the specific project that will be valuated are:

−     Javascript.

Most of visualizations that will be developed would either be part of web applications or visualized with the help of a web browser so the language used to create them would be JavaScript. Having an intermediate/strong experience with JavaScript would be a distinct bonus

−     Graph Databases.

Beginning to intermediate level experience with Graph Databases (Titan, Neo4j and/or Blueprints + Gremlin would be a plus).

−     Java.

The applicant is also expected to have an intermediate/strong experience with programming languages such as Java, (other languages like Scala, Python, C++... are also valuated)

−     Basic knowledge and experience on Linux/Unix

Almost all bioinformatics software and pipelines are used in this operating system.

−     Software engineering.

The applicant should already have experience developing software, ideally a few years

−     Data visualization.

The applicant is expected to have at least some experience on data visualization or capabilities to fast learning it

−     Github experience.

Every piece of software developed at Era7 Bioinformatics is done with the help of Github platform so any prior experience with it would be an advantage

−     Biology background.

Having some sort of biology background would also be a bonus. Being eager to learn and understand the biological part related to the specific visualizations, data analysis workflows and Cloud Computing use created is much more important

−     D3.js experience.

Most of the visualizations created will be based on this technology so any previous knowledge of the library would be a bonus

−     English (C1/C2 level).

The working language at Era7 Bioinformatics research group is English

−     Eagerness to learn technology.

This aspect is crucial for the position. The applicant should be willing and enthusiast to learn cutting-edge technologies during the project.

How to Apply

Application should include:

−     Your letter of motivation

−     CV including your e-mail address and other contact data as well as contact details of 1-3 referees who already know you as a student or employee

−     Examples of software developed, if any

−     List of publications including submitted or in press papers, if any

−     Transcript of BSc or MSc diploma or equivalent.

Applicants should send their application to Eduardo Pareja, [email protected] or [email protected].

The deadline for applications is April 15, 2015. We will assess all applicants within 1-2 weeks after the deadline and conduct telephone or Skype interviews with shortlisted candidates immediately after the assessment.

Successful candidate will be offered PhD positions and instructed about further enrolment formalities. We expect the student to be enrolled in the PhD program and moved to Spain by early-late summer 2015 at the latest. English is the official work language at the Era7 Bioinformatics research group.

You are welcome to address any questions about application process, project, BIG4, or work and life conditions directly to Eduardo Pareja.

About Our Organization

Era7 Bioinformatics is a leading company in Next Generation Sequencing services

Next Generation Sequencing is a huge revolution in DNA sequencing impacting a large number of biomedical, biotechnological and industrial activities.

Our mission is to help our customer to obtain the maximum value from their NGS projects. For that purpose, we offer help in all the steps of the NGS project being a partner for the complete NGS project.

Our business model is based on:

  Research

We think that being ourself researchers (see our research activity here) not only we improve our services every day but we know better the needs of our customers.

  Open Source

We think that today’s bioinformatics is only possible being Open Source

  Cloud Computing

IaaS (Infrastructure as a Service) by means of the use of Amazon Web Services (AWS) leads to real scalability and low cost for our customers. See more here.

  Integrated Services

We know that the goal of a project is to gain knowledge and for that , it is very important to design accordingly the project, to get a sequence of high quality, to analyze it in best possible way and to be able of managing the results easily. Thus, we like to help along all the processcollaborating to the success of the project.

 

But the key for us is our Team.

A young, multidisciplinary and enthusiastic group of people which enjoys working with sequences.

 

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