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New position Open: IT support and software development for the Electron Microscopy Facility.

IT support and software development for the Electron Microscopy Facility of the Natl. Center of Biotechnology (CSIC), Madrid

Description: We are looking for a candidate with a BSc in Computer Science, Mathematics, Engineering, Physics or equivalent, who has experience in system management and software development skills (Python and C/C++). The candidate will be part of a team in charge of managing the cryo-electron microscopy facility’s computing infrastructure and coordinating and assuring the code’s quality developed by the rest of the group (Xmipp, http://xmipp.cnb.csic.es). 

Background: Electron microscopy is currently the most rapidly growing Structural Biology technique. The Natl. Center of Biotechnology (CSIC) hosts the most advanced Cryo-Electron Microscope for Biology in Spain and the Instruct Image Processing Center, a key developer of both XMIPP and Scipion software. Data management and computation are real issues when several Terabytes of images are produced every day in modern cryo Electron Microscopy Facilities.

For further information, go to INSTRUCT Image Processing Center or  Cryo-Electron Microscopy websites.

Location: Madrid 

Required Skills:
-> BSc / MSc in Computer Science, Mathematics, Engineering, Physics or equivalent.
-> Programming experience with python and C/C++
-> Automation skills (bash, python, …)
-> Experience in Linux
-> Experience in the definition and management of computer networks
-> Interest and 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, …).
-> Experience with Graphical Processing Units (GPU) programming
-> Experience in Cloud (Amazon AWS)
-> Experience in team coordination and releasing software
-> Spanish

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

Instruct virtual course on Single Particle Analysis by CryoEM. Madrid, December 14 – 18, 2020

Venue

Remote course
December 14-18, 2020 from 09.30-18.00 CET

Overall aims and course outline

Cryo-Electron Microscopy has established as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and it is capable of accessing to the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like PDB.

The aim of the course is to give an overall overview of the whole process of single particle analysis (SPA) starting from sample preparation, image acquisition at the microscope, image processing and atomic modelling. The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand. In this edition of the course we have included the sample preparation and image acquisition part, which will be done in the recently established high-end CryoEM facility at the CNB, which incorporates a Thermofisher Talos Arctica (200kV) and JEOL CryoARM 300 (300 kV). The CNB CryoEM facility is in the process of being incorporated into the offer of the Instruct catalogue. For this reason, we have extended our traditional 3 days course into a 5 days course that includes sample preparation and image acquisition.

For logistic reasons and travelling restrictions, the whole course will be given online. An additional benefit of this circumstance is that the course can be recorded and stay as a permanent course in Instruct. Although the course is online we will try to keep the interactions with attendees. For this reason, we will limit the maximum number of attendees to 20.

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.

Expected impact for young researchers

CryoEM is the most rapidly growing structural technique. PhD students as well as young post-docs will certainly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Contacts

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors
Marta Martínez (MM), Carlos Oscar Sorzano Sánchez (COSS), Roberto Marabini (RM), Roberto Melero (RME), Jose-María Carazo (JMC), José-María Valpuesta (JMV), Javier Chichón (JC)

Program

Day 1: Data acquisition
9:30       Introduction to the course (JMC, JMV, COSS)
9:35       Introduction to CryoEM (JMV)
10:20     Break
10:30    Introduction to camera detectors (JC)
11:20    Break
11:30    Sample preparation NEGATIVE STAIN (JMV)
12:30    Lunch Break
13:30    Sample preparation VITRIFICATION (JC)
14:20    End of day 		Day 2: Data acquisition
9:30       Data Acquisition Lecture
10:20    Break
10:30    Grid Clipping and Microscope loading (JC)
11:20    Break
11:30    Screening
12:30    Lunch Break
13:30    General discussion
14:20    End of day
Day 3: Data processing
9:30    Movie alignment, Screening micrographs and
CTF (COSS)
10:20  Break
10:30  Particle picking and screening (COSS)
11:20  Break
11:30  2D classification (COSS)
12:30  Lunch Break
13:30  Personal practice
16:30  General discussion
17:00  End of day
Day 4: Data processing
09:30    Initial volume (COSS)
10:20    Break
10:30    Alignment, classification, and
reconstruction (COSS)
11:20    Break
11:30    Validation and analysis  (COSS)
12:20    Lunch Break
13:30    Personal practice
16:30    General discussion
17:00    End of day
Day 5: Data modelling
09:30    Homology modelling (MM, RM)
10:20     Break
10:30     Model alignment and refinement (MM, RM)
11:20    Break
11:30    Model validation (MM, RM)
12:20    Lunch Break
13:30    Model validation (MM, RM)
14:30    General discussion;
Dissemination: Infrastructure access through
Instruct and iNext-Discovery (RME, JMC, COSS)
14:30    End of day work* 		* Virtual machines and I2PC staff will be available
until 17:30 for those who want to access.

Key dates:

October 26 – November 20, 2020: Submission of the course application
23– 30 November, 2020: Communication of awarded applications  

REGISTRATION

Registration will be free for all attendees.
Fill  your application here.  (Registration is now closed)

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project

I2PC Webinars

For a theoretical and practical background on image processing using Scipion, Xmipp and other tools available through Scipion, the Instruct Image Processing Center (I2PC) is organizing short Webinar cycles.

There will be two cycles: New image processing workflows, and Scipion’s tools.

Webinars will be available through the CSIC Conecta platform every Fridays at 17.00 PM CEST with a maximum duration of 1h:

May 29th.
From movies to particles.
Speaker: Carlos Oscar S. Sorzano
Online Registration for this Webinar.
To access the recording of the Webinar click here

June 12th.
From particles to structure.
Speaker: Carlos Oscar S. Sorzano
To access the recording of the Webinar click here

June 26th.
Local resolution tools.
Speaker: Jose Luis Vilas
To access the recording of the Webinar click here

July 10th.
How to install Scipion 3.
Speaker: Pablo Conesa
To access the recording of the Webinar click here

July 24th.
Stream processing in Scipion.
Speaker: David Maluenda
To access the recording of the Webinar click here

Links will be provided after registration

Cryo-EM installed at Instruct Centre ES

08-Apr-2020

A new, state-of-the-art cryo-electron microscope (cryo-EM) has been installed at Instruct Centre ES following a joint, eight-million-euro investment of the Spanish National Center for Biotechnology (CNB-CSIC) and EU structural funds. The JEOL JEM-Z300FSC (CRYO ARM™ 300) microscope, housed at the CNB-CSIC in Madrid, is the first of its kind to be installed in Spain. The new microscope, together with new correlative microscopy facilities, will be made available to Spanish users and also to European researchers through Instruct-ERIC, for a variety of scientific projects.

“The new cryo-EM facility at the CNB-CSIC intends to provide service to the large community of Spanish structural biologists which was in need of adequate infrastructure, but also help both the European academia and industry through its connection with Instruct” remarked Prof José María Valpuesta, director of the cryo-EM facility at CNB-CSIC.

You can access the entire article at: https://instruct-eric.eu/news/state-of-the-art-cryo-em-installed-at-instruct-centre-es/

2nd Scipion Facilities Course (online edition). Madrid, 2020.

Dates:

Tuesday 27 Oct – Friday 30,  4 days, afternoon from 16:00-18:00 CET

Aim

The aim of this meeting is to show what scipion offers to a Cryo-em facility. The course will have a strong “practical component”, since workflows will be running live on the Amazon cloud.

I2PC is organising a Cryo-EM Scipion course specifically for Facilities. Scipion team and collaborators have been working in the last years in what we call streaming processing. We understand the importance of monitoring the acquisition in real time to take early decisions to improve the acquisition performance. In addition, Scipion incorporates new techniques to automate the real time image processing pipeline until 2D classification and even an initial estimation of 3D heterogeneity. Moreover, Scipion is equipped with several consensus protocols to get combined results from different EM-packages to screen and select the best micrographs, CTFs, particles or 2D-classes. All with the benefit of Scipion flexibility and ”mix and match” capabilities. Scipion is also able to gather all the processing information and present it in a HTML report that could be served over the web and automatically refreshed. It also offers automatic tools for direct submission to databases, like EMPIAR, when appropriate.

No programming skills are required.

Target Audience:

Cryo em facility operators wanting to do or already doing on the fly processing. The course will address both Single Particle Analysis (SPA) and Tomography, although the stress will be in SPA.

Conditions: 

Course will be online, so attendees should connect remotely and have internet connection and a modern browser.
No programming skills are required.
AWS machines will be provided by us.

Content

Day 

Time (CET time zone)

Description

Speakers

Tuesday 27th October

16:00-17:00

Welcome, introduction , agenda, logistics.

Jose Maria, Pablo 

 

17:00-19:00

On AWS:  running streaming demo  – intro, file formats,  installation  – plugins – configuration.

Pablo Conesa

Wednesday 28th October

16:00-19:00

Available functionality:  guided practice: from movies to …X.

Consensus.

Breaking the stream.

Marcos, Coss

Thursday 29th October

16:00-18:00

Monitoring – HTML – Grafana (customization) 

Roberto

 

18:00-19:00

Catch-up, personal work

All

Friday 30th October

16:00-17:30

Kicking off scipion (templates) – passing data to user.

Jorge, David

 

17:30-18:30

Submission to EMPIAR, Json summary.

Laura

 

18:30-19:00

What do you miss in the Scipion/your pipeline?

Feedback, open discussion, closing session.

All

Key dates:

01 – 30 September, 2020: Submission of the course application

01 – 15 October, 2020: Communication of awarded applications

Fill  your application here. (Registration will be open soon)

Instruct Course on the development of image processing workflows in streaming and structural data analysis components for Electron Microscopy. Madrid, October 26-30, 2020. (Online edition)

Venue

Remote course (TBA)
October 26-30, 2020 from 15.00-18.00 CET

Overall aims and course outline

Electron microscopy is a well-established and rapidly growing structural technique. There are some consolidated software packages like Relion, Xmipp, Cistem, Eman, IMOD, TomoJ, … that address the image processing steps required for single particle analysis and electron tomography. There are also independent software tools that address a particular and isolated task like movie alignment, CTF determination, particle picking, etc. Software platforms like Scipion facilitate the integration of packages from many different laboratories, and promote the cross-checking of the results by alternative methods. Additionally, Scipion keeps track of all the operations, parameters and steps undertaken from the raw data to the final maps and models, promoting, in this way, the reproducibility of the results. Scipion is used at individual laboratories and at general cryoEM Facilities worldwide. Scipion is quickly expanding to cover the atomic modelling steps and, more recently, tomography software. 


This course will show how to integrate into Scipion any software related to electron microscopy data analysis. You will learn the basic Scipion architecture and to construct a fully functional plugin containing the main elements: protocols, viewers and wizards. The course is aimed at programmers, engineers, computational scientists, physicists, mathematicians, and in general to information technology related scientists with interest in integrating their ideas or software into Scipion. Especially welcome are those developers of software packages or independent software tools for Electron Microscopy. It is suggested that attendees come with their own computer in which they can install software development tools.

 

Target Audience

Software developers interested in developing a Scipion plugin or integrating their software in Scipion.

Conditions

Remote course
Medium programming skills are required:

Python skills are desirable.

AWS machines might be provided by us.

If you want to use your own laptop for development instead of you may need:
 – OS Linux (Ubuntu recommended)
– CUDA (if you have a GPU)
 – python3
 – Conda or miniconda (optional, otherwise we will use virtualenv)

Contact

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Pablo Conesa
email: pconesa@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

I2PC staff: Carlos Oscar Sanchez-Sorzano (COSS), David Maluenda (DM), Jorge Jiménez (JJ), Pablo Conesa (PC), Roberto Marabini (RM), Yunior Fonseca (YF). 

Other tutors: José Miguel de la Rosa Trevín (JMRT from SciLifeLab in Stockholm), Grigory Sharov (GS from MRC-LMB in Cambridge)

Program

You can access the program here.

 

Key dates:

01 – 30 September, 2020: Submission of the course application

01 – 15 October, 2020: Communication of awarded applications  

REGISTRATION

Registration will be free for all attendees.

Fill  your application here. (Registration is now closed) 

 
This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project.

System Manager at the INSTRUCT Image Processing Center (I2PC), CNB-CSIC, Madrid

Description: We are looking for a candidate with a BSc in Computer Science, Mathematics, Physics or equivalent, who has hands-on experience with scientific computing at HPC scale. The candidate will be part of the Biocomputing Unit (BCU) at the National Centre for Biotechnology (CNB-CSIC) where the main task will be to manage the computing infrastructure (on site and remotely) and assist in the deployment and configuration of scientific software.

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 Center for Image Processing in Biology”.
BCU is well known in the area of 3D-EM, with over 200 publications in the area and huge contributions to open source scientific software, like Scipion and Xmipp.

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

Location: Madrid 

Required Skills:

    • BSc / MSc in Computer Science, Mathematics, Physics or equivalent.
    • Automation skills (bash, python…)
    • Experience in Linux and HPC environments
    • Experience with Graphical Processing units (GPU) 
    • 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…).
      • Experience in Virtualization: Docker, Virtualbox
      • Experience as Storage Administrator (SAN / NAS, distributed filesystems)
      • Experience in Cloud (Amazon AWS)
      • Experience in Purchase Management (public sector)

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

2nd Edition of the Instruct course on Image Processing for Electron Microscopy and hybrid modelling. Madrid, September 10 – 13, 2019

Venue

National Center for Biotechnology (CNB), Madrid, Spain

Madrid, September 10 – 13, 2019

Overall aims and course outline

Software platforms as Scipion facilitate the integration of packages from many different laboratories, and promote the cross-checking of the results by alternative methods. Additionally, it keeps track of all the operations, parameters and steps undertaken from the raw data to the final maps and models, promoting, in this way, the reproducibility of the results. Scipion was originally designed to support image processing operations in Single Particle Analysis. However, due to the widespread need to related quasi atomic Coulomb potential maps and model building, with an ever growing potential of simultaneously combining features of both, Sicipion is currently being extended into the atomic modelling domain. In this way it integrates software like Coot, Chimera, Refmac, and Phenix, and the number of integrated packages and procedures is quickly growing. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.

The course is interesting for users to know the image processing and the atomic modelling capabilities of Scipion. This course will bring a timely introduction to these possibilities to investigators at all levels (Ph.D. students, postdocs and senior researchers).. (Note: all practical work will be performed on Amazon cloud, and attendees are required to bring their own personal computer to access the cloud via a web browser).

Contact

Lead contact: Carlos Oscar Sorzano Sánchez
email: coss@cnb.csic.es

Administrative Contact: Blanca Benitez
email: blanca@cnb.csic.es

 Programme

Tuesday, September 10:

13:00 Lunch and registration
14:00 Introduction to the course (Jose Maria Carazo)
14:15 Introduction to 3D EM (Jose Maria Carazo)
15:00 Basic background: sampling, Fourier Transform, central section, sampling, CTF (Carlos Oscar Sorzano)
16:00 Coffee/tea
16:30 Movie alignment, quality estimation, CTF determination (Carlos Oscar Sorzano)
18:30 End of day

Wednesday, September 11:

09:00 Particle picking and particle screening (Carlos Oscar Sorzano)
11:00 Coffee/tea
11:30 2D Classification (Carlos Oscar Sorzano)
13:00 Lunch
14:00 Initial volume, 3D alignment and reconstruction (Carlos Oscar Sorzano)
16:00 Coffee/tea
16:30 3D Classification (Carlos Oscar Sorzano)
18:30 End of day

Thursday, September 12:

09:00 Resolution and quality assessment (Carlos Oscar Sorzano)
11:00 Coffee/tea
11:30 Structure prediction by sequence homolohy (Marta Martínez and Roberto Marabini)
13:00 Lunch
14:00 Rigid fitting (Marta Martínez and Roberto Marabini)
16:00 Coffee/tea
16:30 Flexible fitting (Marta Martínez and Roberto Marabini)
18:30 End of day

Friday, September 13

9:00 Structure validation and comparison (Marta Martínez and Roberto Marabini)
11:00 Coffee/tea
11:30 Building the unit cell and the whole macromolecule (Marta Martínez and Roberto Marabini)
13:00 End of course

Registration Fee:

Academic Registration Fee Instruct countries
Predocs 100 €
Postdocs and Others 150 €
Academic Registration Fee Non Instruct countries
Predoc 150 €
Postdocs and Others 200 €
Industrial Registration Fee 500 €

Payment information

Bank transfer to Centro Nacional de Biotecnología – CNB
Bank Name: Santander Central Hispano

Address: Julio Palacios, 23. 28029, Madrid. Spain

Account: 0049 5926 41 2816155571

IBAN: ES91 0049 5926 4128 1615 5571

Swift: BSCHESMM

Please include your name in the wire concept

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe.

 

Python developer position open

We are seeking python developers to join our Scipion team in Madrid. The team owns and develops an open-source image-processing platform widely used on biomedicine. The lab is involved in several European and Spanish National Research Projects and its software is extensively used in many top institutions all over the world with a high impact on the scientific community. The lab team is rapidly growing and has a high projection in the biomedical research arena. You will become part of a scientific and professional software development team, involved in a wide range of international and cutting-edge initiatives and many opportunities for furthering your knowledge of software development. You will be contributing to all parts of the development process and offering strong technical designs and enhancements. We work openly with our code hosted on GitHub and the majority of our development work is publicly available.

Candidate should have:

– B.Sc., Master, Engineer
– Experience with *nix environments
– Strong programming skills and good level of python
– Git
– Good English level.

Will be valued:

– Experience in Cryo-EM image processing
– Structural biology knowledge
– Experience on scientific computing
– Spanish
– Test automation (buildbot)
– Web development experience

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

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