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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!

biocomputing unit server rack

Description

We are looking for a candidate with a background in Computer Science for the position of Junior 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)
  2. Scripting and orchestrating experience: Bash and Python scripts, YAML (Ansible and similar)
  3. Experience and commodity in Linux environments (HPC environments is a plus)
  4. Interest and/or experience in computer hardware and computer networks
  5. 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…).
  2. Experience in Virtualization: Docker, Virtualbox
  3. Familiarity with the architecture and functioning of GPUs: NVIDIA CUDA, CUDA Toolkit, NVCC…
  4. Experience in Cloud (Amazon AWS)

Applying

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

Diseño estadístico de experimentos con animales

Lugar: Centro Nacional de Biotecnología, C. Darwin, 3, Fuencarral-El Pardo, 28049 Madrid – Sala B.6

Fecha: 11 de octubre de 2024

Este evento está dirigido a los asesores estadísticos que colaboran con comités de ética en experimentación animal y tiene como objetivo explorar y mejorar las prácticas de diseño estadístico en este ámbito. Durante la reunión, discutiremos cómo optimizar los diseños experimentales a través de cursos de formación y recursos comunes. También abordaremos el uso de programas específicos para solicitantes y la creación de un foro de dudas para el diseño experimental. Además, presentaremos la plataforma 3Rs, enfocada en la reducción del uso de animales en la investigación, y exploraremos la posibilidad de organizar un curso de verano para profundizar en estos temas. Únete a nosotros para compartir experiencias, aprender y contribuir a prácticas más éticas y efectivas en la experimentación animal.

Contenido

  • Intercambio de experiencias y mejores prácticas
  • ¿Cómo se puede mejorar el diseño estadístico de los experimentos? ¿Cursos existentes? ¿Formación online asíncrona?
  • ¿Foro de dudas de diseño?
  • Recursos comunes
  • Programas que pueden usar los solicitantes
  • Curso de verano
  • Participación plataforma 3Rs (Reducción) diseño experimental

Agenda

10:00 – 10:15Presentación de la jornada
10:15 – 11:30Presentaciones de los asistentes
11:30 – 12:00Café
12:00 – 14:00Discusión

 

PhD position in Single Particle Analysis and CLEM Correlative Imaging.

Description: We are looking for a candidate with a PhD in Computer Science, Mathematics, Engineering, Physics or equivalent with software development skills, preferrably applied to Structural Biology, Biomedical Imaging, or Imaging in general.

The candidate will work on the development of image processing algorithms for Single Particle Analysis (especially, continuous heterogeneity analysis) and CLEM Correlative imaging (especially, image alignment and segmentation). The contract is for 4 years and will be developed along with Dr. Eva Nogales (from Univ. Calif. Berkeley) in the context of the JAE-CHAIR grant “ALLCRYO. Technical developments for the improvement of the cryoEM workflow, and their application for the structural characterisation of conformationally and compositionally heterogeneous samples in vitro and in vivo.

Location: Madrid

Required Skills:

  • PhD in Computer Science, Mathematics, Engineering, Physics or equivalent
  • Programming experience with Python
  • Experience in Linux
  • Experience in Structural Biology, Biomedical Imaging, General Imaging or Bioinformatics

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

PhD position in fluorescence microscopy image processing.

The Biocomputing Unit of the National Biotechnology Centre is looking for excellent master students in Engineering, Physics, Mathematics or any other field related to data analysis. The PhD would be in fluorescence microscopy image processing.

This project involves several fast-growing technologies: electron cryo-microscopy and deep learning. Our laboratory is located at the Centro Nacional de Biotecnología in Madrid, a reference institute in Spain in cryo-EM, with highly advanced fluorescence microscopy facilities. Moreover, our group is a world reference in this field. In this work we intend to follow two main lines of work:

  • Spatio-temporal analysis, which will allow a more accurate detection and quantification of dynamic phenomena at the cellular level, thus facilitating the exploration of complex biological processes in real time
  • Correlative microscopy: To implement and refine correlative microscopy techniques to efficiently integrate data obtained through different fluorescence microscopy modalities, as well as scanning electron microscopy (SEM) and transmission electron microscopy (TEM).

Latest publications

  1. Cayuela, P. Conesa, A. Oña, J.A. Gómez-Pedrero, C.O.S. Sorzano. Real-Time Correction of Chromatic Aberration in Optical Fluorescence Microscopy. Methods and Applications in Fluorescence, 11: 045001 (2023)
  2. Cayuela-López, J.A. Gómez-Pedrero, A.M. Oña Blanco, C.O.S. Sorzano. Cell-TypeAnalyzer: A flexible Fiji/ImageJ plugin to classify cells according to user-defined criteria. Biological Imaging, 2: e5 (2022)
  3. Cayuela, E. García-Cuesta, J.A. Gomez-Pedrero, S.R. Gardeta, J.M. Rodriguez-Frade, M. Mellado, C.O.S. Sorzano. TrackAnalyzer: A Toolbox for a holistic analysis of Single-Particle Tracks. Biological Imaging, 3: e18 (2023)

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

Artificial intelligence for macromolecular analysis and pharmaceutical ligands design

What we are looking for : We are looking for PhDs in engineering, physics, mathematics, computing science or any related scientific domain with a strong will to apply the AI methods to Structural Biology and Drug Screening. Knowledge of Python and Deep learning libraries are a must. Previous knowledge of Bioinformatics or Biology is highly appreciated, although not compulsory. The Postdoc must propose a research proposal aligned to the presented challenge.

The context : Structural biology is key to understanding biological macromolecules like proteins and nucleic acids, crucial for biological functions and diseases. Cryo-electron microscopy (cryoEM) revolutionizes this field by visualizing macromolecules at near-atomic resolution, facilitating their study in native states. Simultaneously, computational prediction of ligand binding is vital for drug discovery, helping identify therapeutic candidates by how they interact with biomolecules. The synergy of AI tools for cryoEM and ligand prediction accelerates understanding biological systems and developing new treatments.

 

The problem to address : The journey from pixelated snapshots to precise atomic models is fraught with computational hurdles, requiring a blend of innovative AI techniques and a deep understanding of molecular landscapes. Parallel to this endeavor is the quest to discover ligands that snugly fit into these newly revealed structures, a critical step in the design of new drugs. This challenge involves sifting through vast chemical libraries to find those rare molecules that can bind with high affinity to target sites on the macromolecule.

 

Objectives:

  • Elucidating the complex structures of biological macromolecules from CryoEM images.
  • Discover ligands that fit into the structures revealed for new drug design.

 

Expected Outcomes: Robust algorithms and workflows to tackle both problems.

New position open: Software Developer in the Biocomputing Unit (BCU), Instruct Image Processing Center (I2PC), Madrid

Description: We are looking for a candidate 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

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