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

Position Open in image processing for Cryo-Electron Microscopy at BCU

The Biocomputing Unit (BCU) of the Natl. Center of Biotechnology is looking for a candidate with a background in Engineering, Physics, Mathematics or any other data analysis related field. The work is about the development of image processing in Cryo-Electron Microscopy (CryoEM) with a special emphasis on signal processing and efficient implementations. Our laboratory is located at the National Center of Biotechnology in Madrid, a reference institute in Spain in cryo-EM equipped with two microscopes with direct detector (Talos Arctica and CryoARM 300) and a FIB-SEM microscope, providing a very immersive and interdisciplinary environment. Additionally, our group is a world reference in this domain, and the work will be performed in conjunction with an American/Canadian drug discovery company. The goal of the project is to construct the most efficient 3D reconstruction algorithm available for CryoEM.

Recent publications:

FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation. Ramírez-Aportela E, Maluenda D, Fonseca YC, Conesa P, Marabini R, Heymann JB, Carazo JM, Sorzano COS. Nat Commun. 12(1):42. 2021.
DOI: https://doi.org/10.1038/s41467-020-20295-w

Measuring local-directional resolution and local anisotropy in cryo-EM maps. Vilas JL, Tagare HD, Vargas J, Carazo JM, Sorzano COS. Nat Commun. 11(1):55. 2020.
DOI: https://doi.org/10.1038/s41467-019-13742-w

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Melero R, Sorzano COS, Foster B, Vilas JL, Martínez M, Marabini R, Ramírez-Aportela E, Sanchez-Garcia R, Herreros D, Del Caño L, Losana P, Fonseca-Reyna YC, Conesa P, Wrapp D, Chacon P, McLellan JS, Tagare HD, Carazo JM. IUCrJ. 7(Pt 6):1059-69. 2020.
DOI: https://doi.org/10.1107/S2052252520012725

Measurement of local resolution in electron tomography. Vilas JL, Oton J, Messaoudi C, Melero R, Conesa P, Ramirez-Aportela E, Mota J, Martinez M, Jimenez A, Marabini R, Carazo JM, Vargas J, Sorzano COS. J Struct Biol X. 4:100016. 2019
DOI: https://doi.org/10.1016/j.yjsbx.2019.100016

DeepRes: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps. Ramírez-Aportela E, Mota J, Conesa P, Carazo JM, Sorzano COS. IUCrJ. 6(6): 1054 – 1063. 2019
DOI: https://doi.org/10.1107/S2052252519011692

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

PhD. position in image processing for Cryo-Electron Microscopy

The Biocomputing Unit of the Natl. Center of Biotechnology is looking for excellent master students in Engineering, Physics, Mathematics or any other data analysis related field that can compete for FPU fellowships: (https://www.educacionyfp.gob.es/servicios-al-ciudadano/catalogo/general/99/998758/ficha/998758-2020.html). The Ph.D. would be about the development of deep learning methods for image processing in Cryo-Electron Microscopy. This project involves several quickly growing technologies: cryo-electron microscopy and deep learning. Our laboratory is located at the National Center of Biotechnology in Madrid, a reference institute in Spain in cryo-EM equipped with two microscopes with direct detector (Talos Arctica and CryoARM 300) and a FIB-SEM microscope, providing a very immersive and interdisciplinary environment. Additionally, our group is a world reference in this domain.

Recent publications:

(1) FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation. Ramírez-Aportela E, Maluenda D, Fonseca YC, Conesa P, Marabini R, Heymann JB, Carazo JM, Sorzano COS. Nat Commun. 12(1):42. 2021

DOI: https://doi.org/10.1038/s41467-020-20295-w

(2) Measuring local-directional resolution and local anisotropy in cryo-EM maps. Vilas JL, Tagare HD, Vargas J, Carazo JM, Sorzano COS. Nat Commun. 11(1):55. 2020

DOI: https://doi.org/10.1038/s41467-019-13742-w

(3) Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Melero R, Sorzano COS, Foster B, Vilas JL, Martínez M, Marabini R, Ramírez-Aportela E, Sanchez-Garcia R, Herreros D, Del Caño L, Losana P, Fonseca-Reyna YC, Conesa P, Wrapp D, Chacon P, McLellan JS, Tagare HD, Carazo JM. IUCrJ. 7(Pt 6):1059-69. 2020

DOI: https://doi.org/10.1107/S2052252520012725

(4) Measurement of local resolution in electron tomography. Vilas JL, Oton J, Messaoudi C, Melero R, Conesa P, Ramirez-Aportela E, Mota J, Martinez M, Jimenez A, Marabini R, Carazo JM, Vargas J, Sorzano COS. J Struct Biol X. 4:100016. 2019

DOI: https://doi.org/10.1016/j.yjsbx.2019.100016

(5) DeepRes: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps. Ramírez-Aportela E, Mota J, Conesa P, Carazo JM, Sorzano COS. IUCrJ. 6(6): 1054 – 1063. 2019

DOI: https://doi.org/10.1107/S2052252519011692

 

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

Position Open: Bioinformatician at Biocomputing Unit CNB

The Biocomputing Unit (BCU) of the National Center for Biotechnology, headed by Drs. Jose Maria Carazo and Carlos Oscar Sanchez Sorzano, works in the area of both experimental and computational structural biology, coordinating Spanish efforts in the European Infrastructure for Integrative Structural Biology Instruct-ERIC

We develop new ways to extract and integrate biomedical information with a structural focus. In particular, and in the context of this position, we develop an integrative environment where both structural models and cryo Electron Microscopy maps are put in the context of multiple other pieces of information as part of an ELIXIR Recommended Interoperability Resource. 

We are looking for a Bioinformatician participating in the development of key components of our Structural Biology tools, specially 3DBionotes

  • Adding new features to
    the platform focusing on added value to a broad spectrum of users.
  • Searching for new data
    sources, dealing with their integration with current data and proposing
    new ways of representation will cover much of the time.
  • Interacting with current
    and potential users.
  • Frequent planning and
    coordination meetings with the rest of the team are expected.
  • Writing reports and
    instruction manuals as well as presenting results to Projects stakeholders
    and the general public will regularly occur.

Required skills:

  • BSc, MSc level or
    equivalent qualification in Bioinformatics, Information Technology,
    Computer Science or a related discipline.
  • Proficiency using a
    command line UNIX/Linux environment.
  • Familiar with main
    programming languages: Python, JavaScript, Ruby.
  • Knowledge of Docker or
    other containerization technologies.
  • Experience of working
    with a high volume of data.
  • Excellent communication
    and presentation skills, including strong written and verbal communication
    in English.

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

  • Knowledge of Structural biology
    and willingness to stay up-to-date.
  • Experience in data
    analysis, reporting and visualization.
  • Knowledge and some degree
    of experience using relational and/or noSQL databases.
  • Web development
    experience.
  • Familiar with producing
    consuming Web Services.
  • Experience with
    international, multi-disciplinary projects.
  • Analytical mind, eager to
    learn and flexible to adapt to a result driven environment.
  • Ability to work both
    independently and as part of a team.

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

Post-doctoral position in STA and SPA image processing.

One is funded by the European Research Council (ERC) and studies EGFRs and associated complexes on the cell membrane. EGFR is a membrane protein of around 200 kDa involved in breast cancer and a target for new therapies. In this study our collaborators at Zurich-ETH produce cryo-ET tilt-series which are then transferred to Madrid for their further image processing analysis.

The other project focuses on the structural analysis of CoV2 variants mapping on the Spike, mostly by Single Particle Analysis methods. The Biocomputing Unit excels in the development of new image processing approaches to tackle hard problems (see some enclosed recent publications).

We are looking for experienced researchers at the postdoc level experts in SPA and subtomogram averaging who would be responsible for image processing (for EGFR) and data collection and image processing (for CoV2), working side by side with other colleagues either developing new image processing methods in XMIPP or engaged in software integration projects in Scipion. Our laboratory is located at the National Center of Biotechnology in Madrid, a reference institute in Spain in cryo-EM equipped with two microscopes with direct detector (Talos Arctica and CryoARM 300) and a FIB-SEM microscope, providing a very immersive and interdisciplinary environment.

Recent publications:

  1. FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation. Ramírez-Aportela E, Maluenda D, Fonseca YC, Conesa P, Marabini R, Heymann JB, Carazo JM, Sorzano COS. Nat Commun. 12(1):42. 2021
    DOI: https://doi.org/10.1038/s41467-020-20295-w
  2. Measuring local-directional resolution and local anisotropy in cryo-EM maps. Vilas JL, Tagare HD, Vargas J, Carazo JM, Sorzano COS. Nat Commun. 11(1):55. 2020
    DOI: https://doi.org/10.1038/s41467-019-13742-w
  3. Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Melero R, Sorzano COS, Foster B, Vilas JL, Martínez M, Marabini R, Ramírez-Aportela E, Sanchez-Garcia R, Herreros D, Del Caño L, Losana P, Fonseca-Reyna YC, Conesa P, Wrapp D, Chacon P, McLellan JS, Tagare HD, Carazo JM. IUCrJ. 7(Pt 6):1059-69. 2020
    DOI: https://doi.org/10.1107/S2052252520012725
  4. Measurement of local resolution in electron tomography. Vilas JL, Oton J, Messaoudi C, Melero R, Conesa P, Ramirez-Aportela E, Mota J, Martinez M, Jimenez A, Marabini R, Carazo JM, Vargas J, Sorzano COS. J Struct Biol X. 4:100016. 2019
    DOI: https://doi.org/10.1016/j.yjsbx.2019.100016
  5. DeepRes: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps. Ramírez-Aportela E, Mota J, Conesa P, Carazo JM, Sorzano COS. IUCrJ. 6(6): 1054 – 1063. 2019
    DOI: https://doi.org/10.1107/S2052252519011692

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

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.

Data Processing Workshop on Cryo-EM applied to macromolecular complexes: single particle analysis and atomic modelling. ITQB-NOVA. 17-20 September 2019

A 3-day Data Processing on Cryo-EM applied to macromolecular complexes: single particle analysis and atomic modelling Workshop will be organized in Oeiras.
The aim of this workshop is to introduce all the steps for image processing and atomic modelling.


The course will be taught using Scipion a software platform that integrates many image processing packages especifically designed for Electron Microscopy Single Particle Analysis. The platform facilitates the interoperability between the different software packages by converting the data and metadata where necessary. Scipion is particularly well suited for working in High Performance Computers and stream processing at the point of acquisition in EM facilities. Scipion keeps track of all the steps performed as well as their parameters. In this way, reproducibility of the results is guaranteed. Scipion is now extended to allow atomic modelling of the 3D map. In this way, the benefits of traceability and interoperability of Scipion has also been brought to the domain of atomic modelling.

ERC-Synegy “HighResCell”- Position Open

En el marco del proyecto ERC-Synegy “HighResCell”, la Unidad de Biocomputación del Centro Nacional de Biotecnología CSIC desearía incorporar a un excelente investigador postdoctoral para adentrarse en un proyecto complejo, en la frontera de la ciencia y de la tecnología, en un equipo puntero de investigación que, específicamente en cryoEM, cuenta con la Universidad de Zurich (Prof. Ohad Medalia) y la Unidad de Biocomputación del CNB (Profs. JM Carazo y Carlos Óscar Sánchez Sorzano).

El proyecto, centrado en los receptores del Epidermial Growth Factor y que cuenta con la experiencia en purificación y marcaje de proteínas del grupo del Prof. Andreas  Plueckthun, estudiará estas proteínas de membrana solubilizadas, en nanodiscos, en vesículas y, de forma muy importante, in situ en la membrana celular. Los estudios estructurales se complementarán con análisis proteómicos a cargo del Prof. Jesper Olsen.

Es indispensable amplia experiencia previa en procesamiento de imagen en Single Particle Analysis e, idealmente, en subtomogram averaging.

Este proyecto se completará con la interacción con la Infrastructura Europea de Biologia Estructural a través del centro Español Instruct Image Processing Center (I2PC).

El investigador seleccionado se integrará en un equipo diseñado específicamente para este proyecto ERC, con expertos investigadores en cryo microscopia e investigadores en formación en el campo de la algorítmica y del software. Su contratación sería con un contrato de Doctor Fuera de Convenio del CSIC, con el grado según su experiencia.

Puede encontrar información sobre el proyecto y la Unidad de Biocomputación en:

ERC-Synegy “HighResCell: https://cordis.europa.eu/project/rcn/223175/factsheet/en

Prof. Andreas Plueckthun: (https://www.bioc.uzh.ch/plueckthun/

Prof. Ohad Medalia:   https://www.bioc.uzh.ch/en/teaching/study-overview/lecturers/ohad-medalia/

Prof. Jesper Olsen: https://www.cpr.ku.dk/research/proteomics/olsen/

Prof. JM Carazo – Prof Carlos Oscar Sorzano: https://biocomputingunit.es/

Instruct Image Processing Center (I2PC):  http://i2pc.es/

Interesados enviar su CV a: blanca@cnb.csic.es

Position Open at BCU

The Biocomputing Unit at the National Centre for Biotechnology (CNB-CSIC) is seeking a candidate to work on the 3DBIONOTES project in the context of ELIXIR. 3DBIONOTES is a framework for the integration of structural and molecular biology with genomic information (parts of 3DBIONOTES have been recently selected as ELIXIR Recommended Interoperability Resources). The candidate will join a multidisciplinary group with a strong publication record.

Job Description

  • Development of the 3DBIONOTES web framework
    • Integration of new biological databases
    • Development of new visualization and analysis tools
  • Maintenance of the 3DBIONOTES compute infrastructure.
  • Further development of 3DBIONOTES API
  • Datamining and statistical analysis of 3DBIONOTES integrated data
  • Attending ELIXIR/INB meetings and conferences
  • Writing manuscripts

Required Skills

  • BSc in Computer Science, Mathematics, Physics or equivalent
  • MSc in Bioinformatics, Biophysics or equivalent
  • Programming experience at least in one of the following languages: Ruby, Python or JavaScript
  • Good communication skills, highly proficient in spoken and written English

 

Please send your application to Blanca Benitez: blanca@cnb.csic.es

Instruct course on Image Processing for Electron Microscopy in the cloud. Madrid, January 17 – 19, 2018

Electron Microscopy (EM) is rapidly growing as a high-resolution technique for structural biology. However, the high price of the electron microscopes is causing the concentration of scientific equipment in a few labs whose access is granted through infrastructure projects, like Instruct. A typical session in one of these high-end microscopes can generate up to 2TB of data per day, which is analysed by the researcher in its home institution. A new data acquisition will be performed when another access slot is granted. In this way, data analysis is coming at bursts, with high computational demands when the data arrives and low activity between acquisitions. Not all laboratories can justify the cost of a computer cluster with the necessary computational capabilities (in terms of number of cores, RAM memory, disk, GPU, …) with this intermittent use. Computer clouds offer a solution to this problem. This computing power is paid only on demand, and when there is no need of a computer for the data analysis, the machine is simply switched off with no associated cost (maintenance, amortization, dedicated installations and personnel, …).

EM software can easily run in the cloud. In fact, Scipion Cloud has been developed as an Instruct Pilot Project, and it is now publically available in the Amazon Cloud. The proposed course will have two aims:

 – The first one will be to show how to create, setup, use, stop and terminate cloud machines, including the appropriate EM software, so that users can easily adapt the computer power to their needs.
 – The second aim of the course will be to work with the course participants over a typical image processing workflow for single particle image processing.

The course will make extensive use of the I2PC software integration framework Scipion, accessing the most widely used software suites in the field, such as EMAN, Relion, Frealign and XMIPP.

The course is open to investigators at all levels. We will work with examples data, but participants can bring their own data to look at if they wish.