News

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):  https://idospece.i2pc.margaro.eus/

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.

Scipion Training 2017 – April 30 – May 4, Leiden (Netherlands)

Image Processing in cryoEM: Quality checks. NECEN Cryo-EM School

In April 2018, a 4-week CryoEM School will take place at The Netherlands Centre for Electron Nanoscopy (NeCEN). From the 3rd until the 26th of April, 6 participants will receive hands-on Titan Krios training from the experienced operators at NeCEN. You can bring your own sample to collect data on.

In addition to the CryoEM School, a week long Image Processing Course will be organised in collaboration with the Biocomputing Unit of the Spanish National Center for Biotechnology (CNB). The data that you collected during the EM School can be processed under the supervision of CNB instructors.

Visit NeCEN’s Cryo-EM page for more information

Scipion Training 2017 – May 8-9, Montreal (Canada)

Canadian Microscopy and Cytometry Symposium – May 9-12, 2017 in Montreal, Québec, Canada.

The field of cryo-EM is living the so-called resolution revolution thanks to a series of technical advantages, and is starting to provide high-resolution reconstructions routinely. However, at present, cryo-EM is not a push-button technique and a lot of experience has to be added to the reconstruction process. In this workshop participants will be exposed to computational methods from most of the best known software packages (Relion, Eman, Xmipp, etc), using the integrating platform Scipion.

Visit Canadian Microscopy and Cytometry Symposium website for more information.

Python Developers position open

Python Developers position open at I2PC in Madrid. Our team owns and develops an opensource
image-processing platform widely used on biomedicine. We are involved in several
European and Spanish National Research Projects and our software is extensively used in many
top institutions all over the world with a high impact on the scientific community.

Find more information here: Python-Developers-position (PDF file)