Highlights Archives - Biocomputing Unit

Systems Manager job position @ Biocomputing Unit

We have a systems manager job position open at the Biocomputing Unit. Get to know it in this post!

Description

We are looking for a candidate with a background in Computer Science for the position of Systems Management. You will be part of the team in charge of managing the computing infrastructure of the group, learning how public science development and compute infrastructures work. The tasks include assisting in the deployment and configuration of hardware and scientific software. Once here, you will also be participating in European and national projects related to cloud and open data technologies. The amount and heterogeneity of servers requires someone capable of thinking out of the box and exercise creativity to solve IT problems in complex scenarios.

Location: in person, UAM campus, Madrid

Background

INSTRUCT ERIC is the European Strategic Initiative in the area of Structural Biology. It is organized as a distributed infrastructure with “Instruct Centers” and the BCU hosts the “INSTRUCT Image Processing Center (I2PC)”. The BCU is well known in the area of 3D-EM, with over 200 publications in the area and large contributions to open-source scientific software, like Scipion, Xmipp and 3DBionotes. For further information go to i2pc.es and biocomputingunit.es webpages.

Required skills

1. Upper cycle in Computer Science related matters (Spanish “FP superior”, BSc, MSc), Mathematics, Engineering, Physics or equivalent are also accepted.
  - - (specialties or mentions related to systems and networks management such as Computer Engineering/Systems administration appreciated)

1. Scripting and orchestrating experience: Bash and Python scripts, YAML (Ansible and similar)

1. Experience and commodity in Linux environments (HPC environments is a plus)

1. Interest and/or experience in computer hardware and computer networks

1. Medium level of proficiency in written and spoken English

Although not essential, we consider the following skills a “plus”:

1. Experience in assisting open-source software development teams (GitHub, documentation, user support, collaboration tools…).

1. Experience in Virtualization: Docker, Virtualbox

1. Familiarity with the architecture and functioning of GPUs: NVIDIA CUDA, CUDA Toolkit, NVCC…

1. Experience in Cloud (Amazon AWS)

Applying

Are you interested in our Systems Manager job position? Send your CV and a letter of interest to blanca@cnb.csic.es.

2 Open Positions: Software Developer at Biocomputing Unit (BCU), Instruct Image Processing Center (I2PC), Madrid

Description: We are looking for two candidates with a BSc/MSc in Computer Science, Mathematics, Engineering, Physics or equivalent with software development skills. The candidate will be involved in European and National projects related to cloud and open data technologies, being part of a team in charge of developing data management software for Instruct facilities.

Thus, the candidate will participate in projects that will shape and influence strategies for making research data generated across the Instruct-ERIC infrastructure FAIR (Findable, Accessible, Interoperable, Reusable). This data transformation will involve considerations of the storage, metadata description and deposition of large datasets for use and reuse including artificial intelligence. These data will come primarily from structural biology but can include data from other diverse research domains.

Background: INSTRUCT ERIC is the European Strategic Initiative in the area of Integrative Structural Biology. It is organized as a distributed infrastructure with “Instruct Centers” and the BCU hosts the “INSTRUCT Image Processing Center (I2PC)”.

BCU is well known in the area of 3D-EM, with over 200 publications in the area of Electron Microscopy and large contributions to open source scientific software, like Scipion, Xmipp and 3DBionotes.

For further information go to INSTRUCT Image Processing Center or Biocomp web sites.

Location: Madrid

Required Skills:

BSc / MSc in Computer Science, Mathematics, Engineering, Physics or equivalent
Programming experience with Python
Experience in Linux
Medium level of proficiency in written and spoken English

The following skills are considered a “plus”, but are not essential:

Experience of the full lifecycle of software architecture, design, and implementation
Experience developing web and desktop Python apps
Knowledge and some degree of experience using relational and/or noSQL databases.
Experience in assisting open source software development teams (GitHub, documentation, user support, collaboration tools…).
Interest or experience in scientific data management
Interest or experience in biological sciences or bioinformatics
Experience in Virtualization: Docker

Interested candidates should send their CV’s and letter of interest to blanca@cnb.csic.es

I2PC – Instruct-RI Hubs hybrid course on Electron Tomography and Subtomogram Averaging. Madrid, December 10 – 13, 2024

VENUE

Hybrid course.
December 10 – 13, 2024 from 16:00 to 21:30 CET.
You do not need to install any special software to connect. A modern browser should be enough.

Overall aims and course outline

By using image processing algorithms, it becomes possible to pinpoint the macromolecules of interest within the electron tomograms. Subsequently, researchers can extract small subtomograms from these locations and identify similar particles, facilitating their averaging and the recognition of diverse conformations. This process, referred to as subtomogram averaging, has played a pivotal role in elucidating an increasing number of macromolecular structures, achieving resolutions ranging from 20 to 3 A.

The course is designed to offer a comprehensive overview of the whole image processing workflow in Electron Tomography (ET). This includes tasks such as aligning the tilt series, reconstructing 3D tomograms, identifying particles, performing subtomogram averaging or even to perform a tomogram segmentation, all inside Scipion integration framework.

With the experience gained in the organisation of virtual and in-person courses, we intend to organise this course in a hybrid format. We will be able to accommodate up to 20 individuals for in-person attendance. However, other 20 participants will attend remotely. In total, we can host 40 attendees.

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures

For more information see:

I2PC – Instruct-RI Hubs hybrid course on Electron Tomography and Subtomogram Averaging. Madrid, December 10 – 13, 2024 – I2PC – Instruct Image Processing Center

Position open: Software Engineer in the Biocomputing Unit (BCU), CNB-CSIC, Madrid

Description: We are looking for a candidate with a BSc in Computer Science, Mathematics, Engineering, Physics or equivalent, who has experience on system management at HPC scale and/or software development skills. The candidate will be part of a team in charge of managing the computing infrastructure of the group, assisting in the deployment and configuration of scientific software and participating on European and National projects related to cloud and open data technologies.

Background: INSTRUCT ERIC is the European Strategic Initiative in the area of Structural Biology. It is organized as a distributed infrastructure with “Instruct Centers” and the BCU hosts the “INSTRUCT Image Processing Center (I2PC)”.
BCU is well known in the area of 3D-EM, with over 200 publications in the area and large contributions to open source scientific software, like Scipion, Xmipp and 3DBionotes.For further information go to INSTRUCT Image Processing Center or Biocomp web sites.

Location: Madrid

Required Skills:

BSc / MSc in Computer Science, Mathematics, Engineering, Physics or equivalent.
Programming experience with python (C/C++ is a plus)
Experience in Linux and HPC environments
Interest and/or experience in computer Hardware
Medium level of proficiency in written and spoken English

The following skills are considered a “plus”, but are not essential:

Experience in assisting open source software development teams (GitHub, documentation, user support, collaboration tools…).
Automation skills (bash, python…)
Experience in Virtualization: Docker, Virtualbox
Experience with Graphical Processing units (GPU)
Experience in Cloud (Amazon AWS)

Interested candidates should send their CV’s and letter of interest to i2pc@cnb.csic.es.