News

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

Registration Open for the Instruct Biennial 2019. 22nd – 24th May, 2019. Alcala de Henares, Madrid, Spain

Instruct Biennial Structural Biology Conference Structural Biology: Deeper into the Cell. 22nd – 24th May, 2019. Alcala de Henares, Madrid, Spain.

The 4th Instruct Biennial Structural Biology Conference will take place in Alcalá de Henares, Spain, from May 22 till May 24, 2019. The historical Alcalá de Henares was the original location of the Universidad Complutense, founded in 1293 and one of the oldest universities in the world, as well as being the birthplace of Miguel de Cervantes. The social programme of the meeting will include a visit to the city, a gala dinner and extensive opportunities to network with the Instruct Structural Biology community.

More Info at: https://instruct-eric.eu/biennial2019

Registration at: Online Registration

Abstract Submision at: Online Submision

2nd I2PC cryoEM Facilities Meeting. Madrid, June 26-27, 2018

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, June 26 – 27, 2018

Summary

I2PC is organising its second Cryo-EM Facilities meeting. The aim is to gather together Cryo-EM Facility managers who want to share their experience, problems and solutions on data handling and processing, using Scipion or not.  

I2PC, as developers of Scipion, has as one of its top priorities the improvement of the functionality that Scipion offers to Cryo-EM Facilities. We will present Scipion and how it is used in several Facilities together with its development Road Map. More importantly, there will be ample time to discuss and present common Facility problems, and hopefully share with others how you are running your Facility.

Contact

Lead contact: Pablo Conesa Mingo
email: pconesa@cnb.csic.es
Administrative Contact: I2pc@cnb.csic.es

Agenda

Tuesday 26th:

12:00- 13:30 Buffet lunch at CNB (buffer time for everybody to arrive. We are 20’ from airport)
13:30-13:45: Introducing the meeting (Jose Maria Carazo)
13:45-14:00: Introduction participants round table
14:00-15:00: Presentation of Scipion – present and future: Sharing experiences and concerns. Update on the previous meeting. (Pablo Conesa)
15:00-15:30: Setting the scene.  Scipion at the CNB Facility (Roberto Marabini)
15:30-19:00: Other Facilities presentations (To be confirmed: SciLifeLab, Diamond, ESRF, CEITEC, McGill, Copenhagen …..)
(Coffee break at 16:00)
19:00: End of the working day. Either go to your hotel or to a tour by Plaza Mayor
20:30 Dinner at La Barraca Restaurant
Restaurant La Barraca http://www.labarraca.es/

Wednesday 27th:

09:00-10:00: All participants:
For each Facility, identify which are your 3 major problems?. Bring 1 slide presenting them.  Chaired by Pablo Conesa
10:00-10:30: A view on EM Facilities main challenges in the coming years (Erik Franken – Thermo Fisher Scientific)
10:30-11:00: Coffee break 
11:00-12:00: Cryo-EM User and Data Management systems. Chaired by Carlos Oscar Sorzano
11:30-13:30: Discussion: Future challenges.

Which data and in which manner to pass data to users
Scalability facing ever increasing data flows
Other?
Chaired by Jose Miguel de la Rosa

13:30 – Lunch at CNB and farewell

Registration:

The registration  period for this meeting will be open from 01 – 30 April, 2018.  We will contact you after May 1st if your application is accepted.

(Registration Close) Fill  your application here.

Logistics

All expenses during the workshop, meals, coffees are covered. Accommodation and travel is not provided, however we will assist you on the bookings if necessary. There is no onsite accommodation and recommended hotels are:

Scipion V1.1 Release

We are very pleased to announce the release of a new version of Scipion. It’s been over a year since the previous and first version and we have been working on 3 main goals for this release:

  • Consolidation: We put and will always put our best effort into making Scipion a robust and reliable software. We have improved performance, usability and fixed multiple bugs.
  • EM packages integration: We have updated several EM packages to their latest versions (relion 2.0.4, ctffind4.1.8) and added new ones (motioncor2, gctf, gautomatch, …). Single movie alignment protocol (as in Scipion 1.0) has been split into several ones for each program.
  • Streaming capabilities: To speed up first preprocessing steps we have enabled Scipion to work in “streaming mode”, allowing users to compute aligned movies and estimate CTF as soon as a movie or micrograph comes out of the microscope PC.

See the full release notes here

Please, go to http://scipion.cnb.csic.es/m/download_form to download the bundles and follow our installation guide

Many thanks too everyone that have contributed to make this happen:

Instruct Image Processing Center staff

Scipion Developer Position Open

In the context of a number of national and international calls/projects, and for incorporation at the Biocomputing Unit of the CNB-CSIC in Madrid, we are seeking for a mixed profile of a CryoEM structural biologist with programing skills, or vice versa. In the absence of one of the skills, you must be ready to learn the other. The team owns and develops an open-source image-processing platform widely used on structural biology. 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.

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. Our code is open sourced and is freely available for the scientific community at Github.

Candidate should have:

– B.Sc., Master, Engineer
–  Experience in Cryo-EM image processing
– Basic programming skills or a strong desire to learn.
– Good English level.

Will be valued:

– Structural biology knowledge
– Experience with *nix environments
– Experience with Python or other programming languages (Java, Javascript,…)
– Experience on scientific computing
– Other languages, especially Spanish.