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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.

Instruct – New Call for R&D and Internships

Instruct provides access to state-of-the-art infrastructure and technology to support research in structural biology.

Our aim is to encourage and facilitate the integrative use of technologies and methodologies that are available at our 16 Instruct Centres around Europe and in Israel. The Instruct Internship Programme funds research visits of 3-6 months duration to Instruct Centres. Internships cover travel plus subsistence of the intern for pre-doctoral early stage postdoctoral fellows. They facilitate valuable collaborations with Instruct research groups applying techniques that are not available in the applicant’s laboratory and the longer duration of awards allows interns to gain in depth experience in the host laboratory. Submissions should specifically focus on the benefit to the applicant’s research.

Call for submissions for Instruct Internship projects 2016 are now invited. For more information and to apply please click here

Instruct has allocated funds to support small pilot research and development projects in any area of structural biology up to a maximum of EUR15,000 per project. Projects should propose basic or applied research which is preliminary in nature with an expectation of collecting data that may be included in support of an application for more substantial funding through conventional routes. Projects that include technology and/or software development are encouraged. All submissions must include the use of technologies available at Instruct Centres through the Instruct access process.

Call for submissions for Instruct pilot R&D project 2016 are now invited. For more information and to apply please click here

Deadline for Internship submission is 5pm CET, Wednesday 31st August.

Deadline for R&D submission is 5pm CET, Friday 30th September.

Applicants must be registered on the Instruct website and be resident in an Instruct member country. The call submission forms and further information are available on the Instruct website. Alternatively if you need additional help you can contact us directly at admin@structuralbiology.eu.

Scipion v1.0.0 released

We are proud to announce the release of Scipion v1.0.0, our software workflow framework to obtain 3D maps of macromolecular complexes that integrates multiple EM software packages.

Scipion is open-source software and can be freely downloaded from Scipion web site. There you will also find the Installation instructions

Scipion’s main features

  1. Integration and Interoperability: Scipion transparently integrates several software packages such as: Xmipp, Relion, Spider, Eman, Sparx, Frealign and Ctffind, among others. Scipion  allows users to easily combine different programs in the same project in the form of a graphical workflow. All required format conversions are done automatically. More than 100 protocols are currently implemented, see the full list of protocols
  2. Traceability and Reproducibility: all parameters used and steps performed are stored! The entire workflow is presented as a tree or as a list. Several steps can be copied and re-executed with different parameters. The workflow, or part of it, can be exported to a template that can imported into a different project. The workflow templateis a text file that can be easily shared (email, http, etc)
  3. Graphical tools: Scipion comes with several built-in graphical tools. All protocols are executed from a form that provides validation and help messages for each parameter. Integrated data viewers can visualize images, volumes, micrographs and their related metadata (shifts, angles, weights, etc). This data viewer is very useful for sets manipulation, also stored as steps in the project history.
  4. Automation and API: all operations can be done from the GUI or from Python scripts. This includes creating a new project, launching runs and repeating previous runs, among others. Developers also have Python libraries to operate with images and metadata files.
  5. Extensibility: Scipion is designed with extensibility in mind. As a result, new algorithms and visualization tools can be added with relative small effort. Everyone is welcome to contribute. A good starting point is the tutorials page.

During this year we will have multiple Scipion workshops. Do not miss your next one!

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