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/
News
Coronavirus alert in Madrid affects the activity of I2PC
Dear Users,
Due the Coronavirus situation in Madrid, our operations have been affected. We will be available only by email. Please contact us at: I2pc@cnb.csic.es.
You can also reach out to your I2PC contact by email.
Apologies for the inconveniences.
I2PC Staff
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
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:
- Hotel Weare Chamartin: http://www.weare-chamartin.com (in Chamartin railway station)
- Hotel NH Madrid Nacional: https://www.nh-hoteles.es/hotel/nh-madrid-nacional (close to Atocha railway station)
