News

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 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 31^st August.

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

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!