News

2017

Instruct Biennial Structural Biology Meeting #IBSBM2017

Brno, Czech Republic, 24th to 26th May 2017

Instruct Biennial Structural Biology Meeting will be held at the International Best Western Hotel, Brno, CzechRepublic. The meeting will showcase integrative structural biology and its impact on biological research. The program will include sessions that represent recent advances in structural biology towards cellular biology, emerging methods and technologies and results of biomedical importance. Young scientists who want to know what structural biology can offer for their research and what are the future trends, are especially encouraged to attend.

Register today

Instruct is a distributed European Research Infrastructure, which provides scientists with access to all major cutting edge technologies that enable biomacromolecular structure determination at atomic resolution. Access to all of these technologies has been available to European member researchers from February 2012

2016

First iNEXT All Hands Meeting

First iNEXT All Hands Meeting. Madrid, 19 - 21 October, 2016.

AHM 2016 is the first annual meeting of iNEXT. It aims at gathering not only iNEXT Partners, but also iNEXT Users (or intended users) contacted directly by the different Facilities in the project. iNEXT Partners, together with the Scientific Advisory Board and the Industry Panel, will review the work performed in the project, including its different Joint Research Activities. iNEXT meeting web page

I2PC-FEI hands on autumn course

First I2PC-FEI “hands on” course on image processing. Madrid, 17 - 20 October, 2016.

The Instruct Image Processing Center at the CNB-CSIC and FEI Corporation joint course aims to provide an in-depth presentation of current image processing methods in cryo-Electron Microscopy. The course will be of a very practical nature. Course web page

CORBEL launches 1st Open Call for research projects

CORBEL – Coordinated Research Infrastructures Building Enduring Life-science services – is an EC Horizon2020 project uniting 11 Biological and Medical Science Research Infrastructures (RIs). In CORBEL, the participating RIs expand their cooperation in order to harmonise researchers’ access to their cutting-edge technologies and services by establishing a sustainable platform of aligned services that will enable faster admission to and a wider portfolio of technologies and services to boost research projects.

The CORBEL Open Call invites researchers to apply to access technologies and services from more than 15 facilities from eight different research infrastructures across Europe. Selected projects will be allocated to so-called Access Tracks and gain unprecedented opportunities to utilise a wide range of high-end technologies and services. These include state-of-the-art offers from the fields of advanced imaging, biobanking, curated databases, marine model organisms, mouse mutant phenotyping, screening and medicinal chemistry, structural biology as well as systems biology.

Projects will be supported at every stage, with CORBEL project managers on hand to help scientists navigate between different service providers and exploit the full potential of the offers available.

Learn more about the CORBEL Open Call by visiting our website (http://www.corbel-project.eu/1st-open-call.html).

I2PC-CCISB hands on spring course

From 2D images to 3D structures: A practical course on Electron Microscopy Single Particle Analysis. Madrid, May 17 - 20, 2016

A joint computational course between the Instruct Image Processing Center (I2PC) and the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM, a member of CCISB). Tutors from Spain and the UK will address the complete image processing workflow typical for macromolecular structural determination, from processing the raw images taken on the electron microscope to the interpretation of the derived 3D volumetric structure.

Scipion v1.0.0 released

Scipion v.1.0.0 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!

2015

I2PC hands-on summer course

I2PC hands on course on image processing applied to the structural characterization of biological macromolecules. Madrid, June 29th - July 3rd, 2015

Instruct Biennial Meeting

Instruct Biennial Meeting logo "Showcasing Integrative Structural Biology". Florence (Italy), 20-22 May 2015

The second Instruct Biennial Structural Biology Meeting will showcase integrative structural biology and its impact on biological research. Register now!

Student fellowships available (deadline Friday 13th March 2015).

Instruct call for proposals

Instruct has 16 Instruct Centres in Europe and Israel offering access to a full range of advanced technologies and expert support.

Access to the infrastructure at Instruct Centres is provided for all Instruct members and there are no charges (consumable costs, accommodation and travel are supported by Instruct funds, up to a maximum of €1100 per visit).

The deadline for this round of proposal submission is 5pm CET, Thursday 30th April 2015. Submit your proposal.

2014

Instruct: Focus on Spain

Spain has been in close contact with Instruct since the early stages of the preparatory phase of this Infrastructure. Membership of Instruct with full rights came only with the signing of the International Consortium Agreement at the First Instruct Biennial Structural Biology Meeting in Heidelberg in May 2013. In the relative short period since the signing of the ICA, Spanish scientists have become the main users of the Instruct access proposal system.

Building on the clearly expressed scientific national interest indicated before, and in spite of the severe national economic recession, Spain is seriously considering being one of the Founding Members of the future Instruct ERIC.

Access Call Open

Call for access is now open. Visit any number of the Instruct platforms to perform cutting edge science.

Submit your proposal for access today. Call closes 30th January 2015 at 5pm CET.

Instruct call for Research and Development pilot projects is now open (June 6th - July 11th)

A maximum of 20,000€ per project will be awarded to support a limited number of pilot studies proposed by researchers from Instruct member countries (BE, CZ, DE, ES, FR, IL, IT, NL, PT, SE, UK). Projects should propose basic or applied research which is preliminary in nature.

The intent of this support is to help researchers develop external funding for projects, i.e. the expectation is that a pilot study will lead to a full grant submission. The funds are expected to cover research expenses but not normally salaries.

More information

Meet us at ICRI 2014

I2PC will be representing Instruct this year at the International Conference on Research Infrastructures (ISCRI 2014), from 2nd to 4th of April.

I2PC welcomes its Strategic Advisory Board

Today, March 18th, we are receiving the Strategic Advisory Board on its visit to the I2PC

2nd Call for proposals to access the full set of Instruct facilities

2nd "Call for proposals utilising Instruct-funded structural biology techniques" (March 5th - April 11th). Proposals for funded access to the full set of Instruct facilities are now invited.

Access to the Instruct Centre technologies is FREE to scientists from Instruct member countries.

Workshop on Algorithms for 3D Reconstruction in Soft X-Ray Microscopy. Madrid, January 20th-21st

An intensive meeting devoted to discuss the image processing challenges raised by recent advances in Soft X-ray tomography of cellular materials at cryogenic temperatures. The topics to be discussed include Image Formation, Depth of Field and Zone Plates, Contrast Enhancement, information Recovery and Tomographic Algorithms.

Electron Microscopy and X-ray Tomography Training Schools.Madrid, January 13th-17th

In the frame of three European projects, the Instruct ESFRI project on Structural Biology, the Biostruct-X project and the COST Action MP1207, the Instruct Image Processing Center at CNB-CSIC is planning training schools on 3D Reconstruction in Electron Microscopy and Soft X-ray Microscopy for January 2014.

The course will focus on image processing topics, introducing the basic principles behind the capacity to achieve quantitative 3D information from sets of images and providing ample time for practical work.

2013

Xmipp Workshop in Paris, November 7th-8th

The Workshop covers the details of the Xmipp software package, that is used for reconstructing 3D maps from sets of individual particle images. The majority of the workshop consists of hands-on sessions designed to familiarize the attendees with the public-domain Xmipp software. Registration and further details

Instruct Initiative users meeting, Valencia 2013

As we previously announced in this web site, Spain formally joined Instruct at a signing ceremony coinciding with the First Biennial Structural Biology Meeting in Heidelberg on the 24th of May 2013.

This meeting will take place as a session of the XIII International Congress of the Spanish Biophysical Society in Valencia (Spain) next week (19th-21st June). The session will be broadcasted live.

New: if you could not attend the live broadcast, we have published the recorded video of the session on YouTube. Download the slides used in the presentation

Spain joins Instruct

In the last two years Instruct has given academic and commercial scientists across Europe access to a full portfolio of integrated technologies, thanks to the collaboration of fifteen of Europe's leading structural biology research institutes.

Today, June 3rd, Instruct is pleased to welcome Spain as a new Instruct member state. Spain joins nine countries that are already members; Belgium, Czech Republic, France, Germany, Israel, Italy, The Netherlands, Portugal and the United Kingdom, ensuring Spanish researchers a single point of access to the technology and expertise offered through Instruct. See MINECO press release

I2PC is attending the First Instruct Biennial Structural Biology Meeting held in Heidelberg, May 22nd-24th

Some pictures from the first and second days of the First Instruct Biennial Structural Biology Conference held in Heidelberg.

Xmipp Workshop in Martinsried, March 12nd-13rd

The Workshop covers the details of the Xmipp software package that is used for reconstructing 3D maps from a set of randomly oriented particle images. The majority of the workshop consists of hands-on sessions designed to familiarize the attendees with the public-domain Xmipp software.

More information

CTF Estimation Challenge

The CTF Estimation Challenge will be run from March 1st to July 15th as a collaboration between researchers, rather than a competition. Each challenger commits to submitting a manuscript to the next I2PC workshop summarizing the method used and results, and later to sharing the results with the community, such that we can foster a fruitful discussion at the meeting. Although several data sets will be made available, participants may choose to process only one data set if they prefer.

A paper summarizing all results will be prepared after the workshop.

We are pleased to announce the CTF estimation challenge called by the Madrid Instruct Image Processing Center (I2PC) in collaboration with the National Center for Macromolecular Imaging at Houston. By participating in this challenge, researchers will have the opportunity to test their ability estimating some of the key parameters of the Electron Microscope Contrast Transfer Function on a large micrograph data set produced by well-known laboratories on a wide set of experimental conditions.

2012

FluoJ

Fluorescence microscopy image analysis is different for each sample but there are usually a common set of steps in the analysis workflow such as image preprocessing, segmentation, specimens characterization and classification.

In FluoJ user configures this steps for each sample and trains the classifier (optional) in order to do automatic image processing and classification. This way a variety of sample studies can be processed improving image analysis and minimizing user intervention. Contact us to try your images.

I2PC Developer Workshop

The first I2PC Developer Workshop will take place in Madrid, 6th and 7th of February. The main objective is to standardize information exchange in Single Particles as well as to start a dynamic of algorithm benchmarking in the field. Concrete conclussions on data interchange were reached and a first benchmarking challenge was issued to the community.

Jose Maria Carazo
Introduction and setting the goals and expectation of this meeting.

Benchmarks

Wah Chiu
Report on Map and Model Validation (from the Validation Task Force)
Christian Blaschke
Introduction to Bechmarking (I): The current situation in Bioinformatics
Adrian Quintana
Introduction to Bechmarking (II): The current situation in other imaging communities
Anchi Cheng
Presentation of Past Particle Picking Benchmark
Steven Ludtke
Presentation of Past Modeling Challenge
Carlos Oscar Sorzano Sanchez
Presentation of Past EU NoE 'intended Benchmark'
Adrian Quintana
Presentation of I2PC Prototype Benchmark Platform
Wah Chiu
Discussion & Conclussions on Benchmark activities in 3DEM

Workflows in Single Particle

Carlos Oscar Sorzano Sanchez
Setting the scene
Standardized Workflows
Robert Langlois
Workflows in Spider
Roberto Marabini
Workflows in XMIPP
Steven Ludtke
Workflows in EMAN
Bernard Heymann
Workflows in Bsoft
Marin van Heel
Workflows in Imagic
Anchi Cheng
Workflows in Appion
Adrian Quintana
Workflows in Scipion
Jose Maria Carazo
Discussion & Conclussions on Workflows
Roberto Marabini
Conclussions on Workflows

Ontologies and Vocabularies

Roberto Marabini
General presentation on Ontologies and information organization. Presentation of the Scipion Ontology
John Westbrook
Vocabularies and Ontologies. The case of the EMDB submission vocabulary
Steven Ludtke
Presentation of the EMEN Ontology (I & II
Jose Maria Carazo & Roberto Marabini
Discussion on Ontologies

PeppeR new release: 1.11.02

A new version of the DAS client for 3D-EM, PeppeR, has been released. PeppeR is the annotation browser for macro-molecular structures that allows to display Hybrid models. These models are obtained by fitting the atomic cordinates derived from X-ray cristallograpgy or NMR; into the 3D volume maps obtained by Electron microscopy.

More details can be seen in the PeppeR home web. Try PeppeR v1.11.02, Now!

2011

3D Electron Microscopy Benchmark Web

3DEM Benchmark website, a joint initiative of the National Institute of Bioinformatics (INB) and the INSTRUCT Center for Image Processing in Microscopy, has been develop to foster the development of new advanced methods in the area of image processing in Structural Biology. To this end we provide a robust computational infrastructure capable of supporting the automatic and standardized benchmarking of image processing applications.