Re: [ccp4bb] Slightly OT: crystallization teaching resources for kids

[Tim Gruene]

Dear Nicolas,

are you sure this concept is correct?

The entropy of molecules arranged in a crystal must be greatly larger than in 
solution. Hence the driving force for crystallisation is actually a drop in 
energy, and I am not sure there is actually a barrier.

I would take the kids to the play ground and let them run around randomly. 
When I blow a wistle they should line up in an orderly manner.

I am sure it will take some time before some sort of order is achieved, for 
the kids could face in various directions, or line up in blocks, or other 
shapes. Once a seed is there, i.e. once e.g. 4-5 kids have created a regular 
block, it will be much easier for the rest to line up (this is consistent with 
Patrick's explanation).

Cheers,
Tim

On Wednesday 04 January 2017 05:45:50 PM Nicolas FOOS wrote:
> Dear Evette,
> 
> If I was is your situation (explaining nucleation and other concept). I
> will discuss in terms of energy.
> 
> I mean obtaining the initial nuclei is the "costly" step in terms of
> energy. To represent that, out the classical curve of energy, I will use
> a metaphoric representation such as jump over a barrier and run after.
> 
> With this analogy, it's possible to explain that the first step is
> difficult and the second more accessible. If the barrier is to high,
> it's impossible to continue and run. If you don't have any barrier it's
> easy to run and if you only have a small barrier is not to difficult to
> jump over and run. But It also allow you to explain that if you
> facilitate the apparition of the first "surface" thanks to appropriate
> method (seeding, dust...) you can help the first step (to continue with
> the barrier story, it like you have ladder to help, or the ability to
> decrease the size of the barrier.
> 
> For why the crystal and how, I will maybe use the example of orange
> pyramid in the food store. Orange are stable together because they have
> enough contact, because they have relatively homogeneous shape. If you
> mixed orange with water melon it's difficult to obtain nice pyramid.
> 
> For crystallization experiment which work, I have no Idea out of the one
> you already mentioned.
> 
> 
> Hope this help.
> 
> Nicolas
> 
> Nicolas Foos
> PhD
> Structural Biology Group
> European Synchrotron Radiation Facility (E.S.R.F)
> 71, avenue des Martyrs
> CS 40220
> 38043 GRENOBLE Cedex 9
> +33 (0)6 76 88 14 87
> +33 (0)4 76 88 45 19
> 
> On 30/12/2016 11:06, Radisky, Evette S., Ph.D. wrote:
> > Can anyone point to some especially useful resources to help explain
> > to kids (pre-chemistry, ~age 10-12) how and why molecules crystallize?
> > Maybe a good online movie or animation?  I am especially needing help
> > with the concept of nucleation, and why nucleation is slower and then
> > crystal growth faster once nuclei have formed.  I have been
> > supervising some experiments growing sucrose crystals from
> > supersaturated solutions, which have worked really well, but I am
> > having more difficulty in explaining the underlying fundamental
> > concepts in a way that is understandable to the kids.
> > 
> > Thanks!
> > Evette
> > 
> > Evette Radisky, PhD
> > 
> > Associate Professor of Cancer Biology
> > 
> > Mayo Clinic Cancer Center
> > 
> > Griffin Cancer Research Building
> > 
> > 4500 San Pablo Road 
> > 
> > Jacksonville, FL 32224 
> > 
> > tel: 904-953-6372 
> > 
> > fax: 904-953-0277 
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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[ccp4bb] Internship at Merck, West Point, PA, USA

[Kaspar Hollenstein]

Dear All,

I would like to bring to your attention the job opportunity outlined below.
Please forward to anyone who might be interested in this 11-12 week
internship at our West Point, PA, USA site (Req ID ADM008072).

IMPORTANT: Please do not reply to this email to apply. Use this link
instead:

https://jobs.msd.com/job/Kenilworth-2017-Structural-Sciences-Protein-Sciences-Internship-Job-NJ-07033/381645700/

Best,

Kaspar


Kaspar Hollenstein | Biochemical Engineering and Structure | Merck & Co.
770 Sumneytown Pike | WP14-1114 | West Point, PA 19486


2017 Structural Sciences-Protein Sciences Internship:ADM008072

Description

Merck & Co., Inc. Kenilworth, N.J., U.S.A. known as Merck in the United
States and Canada, is a global health care leader with a diversified
portfolio of prescription medicines, vaccines and animal health products.
Today, we are building a new kind of healthcare company – one that is ready
to help create a healthier future for all of us.

Our ability to excel depends on the integrity, knowledge, imagination,
skill, diversity and teamwork of an individual like you. To this end, we
strive to create an environment of mutual respect, encouragement and
teamwork. As part of our global team, you’ll have the opportunity to
collaborate with talented and dedicated colleagues while developing and
expanding your career.


The Future Talent Program features internships that last 11-12 weeks and
will include one or more projects. These opportunities in our Merck
Research Labs (MRL) can provide you with great development and a chance to
see if we are the right company for your long-term goals.

The Department of Chemical Capabilities and Screening within Merck Research
Laboratories located in West Point, PA, is seeking an undergraduate summer
intern. The intern will function as a fully-integrated member of a
structural biology team, consisting of X-ray crystallographers, protein
biochemists, and molecular biologists.

The job will involve development of a reference system for
pre-crystallization and crystallization screening of membrane proteins. The
intern will:

- Apply state-of-the art protein expression and purification methods to
generate membrane proteins and membrane protein complexes of sufficiently
high quality for structural studies using X-ray crystallography. Day-to-day
research will focus on using techniques in protein biochemistry and
biophysics to purify and characterize these challenging to work with drug
targets.

- Carry out protein production in prokaryotic and/or eukaryotic expression
systems, preparative protein purification, labeling, characterization using
SDS-PAGE, spectroscopic and analytical chromatographic methods,
pre-crystallization assays, and crystallization screening.

- Be responsible for accurate electronic notebook recording, safe
laboratory practices, and presentation of data and their interpretation to
a team of scientists.

- Attend departmental and team meetings to gain a wider perspective on the
drug development process in the pharmaceutical industry.

We are seeking intern candidates with strong academic performance,
communication skills, teamwork, and the ability to work in a
cross-functional environment.

Location: West Point, PA

This is a full-time paid internship whereby a weekly stipend will be
provided to the student. Housing subsidy is not available as part of this
program, and if housing is required by student, it must be funded 100% by
the student.

**Please note when applying for this position, if candidate is selected for
an interview, applicant must be prepared to submit letters of
recommendation and a brief research statement and a copy of transcript.

Qualifications

Education:

- Required: Currently pursuing a BA/BS degree in Biochemistry.

Required Experience:

- Must have completed a minimum of (2) years of studies towards a BA/BS
degree at time of internship in summer 2017.

- Must be returning to school in Fall 2017.

- Must be available for full-time employment for 11-12 weeks during the
months of June to August 2017

Preferred Experience:

- Significant interest in protein structure/function.

- Basic laboratory skills and research experience such as: molecular
biology, protein expression and purification, protein characterization
using biochemical and biophysical techniques, and safe lab practices.

- GPA of 3.0 or higher

Our employees are the key to our company’s success. We demonstrate our
commitment to our employees by offering a competitive and valuable rewards
program. Our Company’s benefits are designed to support the wide range of
goals, needs and lifestyles of our employees, and many of the people that
matter the most in their lives. If you need an accommodation for the
application process please email us at staffingaa...@merck.com.

Search Firm Representatives Please Read Carefully:

Merck & Co., Inc. is not accepting unsolicited assistance from search firms
for this employment opportunity. Please, no phone calls or 

Re: [ccp4bb] Visualize symmetry operations

[Robert Campbell]

Hi Aaron,

I have a PyMOL plugin based on cctbx (i.e. it requires the installation of 
cctbx) that will do this.  This allows one to make images like this:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/pymol_symmetry.png


The script is called draw_symops_cctbx.py and is available here:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

(this may site may already be listed in the repositories of the PyMOL plugin 
manager).


Cheers,
Rob


On Wed, 2017-01-04 12:38  -0800,  Pavel Afonine  wrote:

> Explore this:
> 
> http://cci.lbl.gov/cctbx/
> 
> Pavel
> 
> On Wed, Jan 4, 2017 at 8:20 AM, Aaron Finke  wrote:
> 
> > Dear CCP4-keteers,
> >
> > Is there a program that can visualize symmetry operation positions
> > (e.g. twofold screws, fourfolds) in protein structures, like CCDC
> > Mercury does for small molecules?
> >
> > Thanks in advance,
> > Aaron
> >
> > --
> > Aaron Finke
> > Staff Scientist, MacCHESS
> > Cornell University
> > e-mail: af...@cornell.edu
> >
> >  




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] Visualize symmetry operations

[Pavel Afonine]

Explore this:

http://cci.lbl.gov/cctbx/

Pavel

On Wed, Jan 4, 2017 at 8:20 AM, Aaron Finke  wrote:

> Dear CCP4-keteers,
>
> Is there a program that can visualize symmetry operation positions (e.g.
> twofold screws, fourfolds) in protein structures, like CCDC Mercury does
> for small molecules?
>
> Thanks in advance,
> Aaron
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
>

[ccp4bb] Integrative Structural Biology, Oléron, France, June 16-23th, 2017

[Jean CAVARELLI]

Dear CCP4

We are pleased to announce the 4th RéNaFoBiS workshop, dedicated to Integrative 
Structural Biology, that will take place on the Oléron island (France), from 
June 16 to June 23, 2017. The main objective of this workshop is to offer a 
theoretical and practical training in the different techniques used in 
integrative structural biology (X-ray diffraction, Small angle X-ray 
scattering, NMR, cryo-electron microscopy, cellular and molecular imaging, 
biophysical methods and macromolecular interactions.) The goals are to explain 
and illustrate, to an audience mainly composed of doctoral students and young 
researchers, the contributions and limitations of each method with a strong 
emphasis on their complementarity and future developments.
The official language of the workshop is French but presentations may be given 
in English, depending on the overall profile of the students. For practicals, 
English and French speaking groups may be organised.

Registration is now open on the web site:
https://ecolebios2017.sciencesconf.org/
Deadline for registration: April 9, 2017 (maximum number of participants: 25)
More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/


Best  regards
Jean Cavarelli
National ReNaFoBiS Coordinator


Professor of Structural Biology
"Structural biology of epigenetic targets"
Department of Integrated structural biology
UMR7104 CNRS-UNISTRA, INSERM U964.
e-mail : c...@igbmc.fr
phone : +33 (0)3 69 48 52 74

[ccp4bb] Emory University: Assistant/Associate Professor in Structural Biology (Tenure Track)

[Ortlund, Eric]

Dear All,

The Department of Biochemistry in the Emory University School of Medicine is 
seeking to hire an Assistant/Associate Professor (tenure track) with expertise 
in structural biology and complementary biochemical/ biophysical approaches. 
The Department of Biochemistry is a leading research division within the School 
of Medicine with particular strengths in the application of structural biology, 
biochemistry and cell biology to understanding diverse fundamental biological 
processes that underpin human health and disease. These include but are not 
limited to the study of gene expression and control of protein synthesis, cell 
signaling, DNA repair and genome stability, and protein/ nucleic acid 
modification (for further details see: http://www.biochem.emory.edu/). Current 
Department faculty also bridge the School of Medicine’s basic research mission 
with other broader initiatives such as the Winship Cancer Institute, Emory 
Antibiotic Resistance Center (Emory ARC), Alzheimer’s Disease Research Center 
(ADRC), and Emory Vaccine and Treatment Evaluation Unit (VTEU) Systems Biology 
Center.

The successful candidate will have a Ph.D. (or equivalent) and postdoctoral 
experience in biochemistry and structural biology, or closely related 
disciplines(s). The selected candidate will be expected to build a dynamic, 
independent research program in the broadly defined area of structural biology, 
preferably using high-resolution single particle cryo-EM, x-ray 
crystallography, and/or single molecule optical microscopy studies, to build on 
Emory’s existing strengths in these areas. Selection criteria for this position 
will include a track record of scientific productivity, as evidenced by primary 
research publications and extramural funding, as well as the candidate’s future 
research vision and potential to contribute the Department’s graduate and 
medical student teaching.

Applicants should compile a single PDF file containing the following 
information:

  1.  Cover letter highlighting key qualifications.
  2.  Current curriculum vitae with complete bibliography.
  3.  Names and contact information of three references.
  4.  A research statement comprising descriptions of past accomplishments, 
including three publications that best epitomize the relevant skills of the 
applicant, and future research goals (3 pages total).

Application materials should be uploaded here:
https://sjobs.brassring.com/1033/ASP/TG/cim_jobdetail.asp?partnerid=25066=5449=67992br

Initial review of applications will begin on February 15, 2017. Applications 
received after this date will be considered on a rolling basis until the 
position is filled.

Emory University is an Equal Opportunity/Affirmative Action/Disability/Veteran 
Employer. Applications from women and underrepresented minority candidates are 
strongly encouraged.

The Department maintains an in-house automated X-ray diffraction system (Rigaku 
MicroMax-007) along with robots for making and setting screens.  We are members 
of the South East Regional Collaborative Access Team at Argonne National Labs 
providing for regular synchrotron access. To support Single Particle CryoEM, 
Emory recently purchased a 120 KV Talos L120C with Ceta 16M Camera and a 200 kV 
Talos Arctica with BioQuantum and K2/K3 Upgrade dedicated to single particle 
studies.

Warmest Regards,

Eric

Eric Ortlund, Ph.D.
Associate Professor
Director of Emory Integrated Lipidomics Core
Department of Biochemistry
Emory University School of Medicine
1510 Clifton Road, NE, Room G235
Atlanta, GA  30322
Tel 404-727-5014  Fax  404-727-2738
eric.ortl...@emory.edu
http://www.biochem.emory.edu/ortlund/






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Re: [ccp4bb] Slightly OT: crystallization teaching resources for kids

[Patrick Shaw Stewart]

Yes, but the kids will want to know WHY there is an energy barrier.

I prefer my explanation below.

Happy New Year to all

Patrick
_

> I am especially needing help with the concept of nucleation, and why
nucleation is slower and then crystal growth faster once nuclei have
formed.

I always explain this by pointing out that, when the crystal is very small,
each new molecule that lands on the surface of the nascent crystal can only
be attached on one or two sides.  When the crystal is larger, molecules
that land are more likely to become attached on two, three or more sides.

Atomic force microscopy images of "islands" that appear on the faces of
crystals are also helpful.  Islands are more likely to appear on larger
faces.  Once they appear they can rapidly spread to the edges of the
crystal, which is (one mechanism explaining) why crystals have flat faces.





On 4 January 2017 at 16:45, Nicolas FOOS  wrote:

> Dear Evette,
>
> If I was is your situation (explaining nucleation and other concept). I
> will discuss in terms of energy.
>
> I mean obtaining the initial nuclei is the "costly" step in terms of
> energy. To represent that, out the classical curve of energy, I will use a
> metaphoric representation such as jump over a barrier and run after.
>
> With this analogy, it's possible to explain that the first step is
> difficult and the second more accessible. If the barrier is to high, it's
> impossible to continue and run. If you don't have any barrier it's easy to
> run and if you only have a small barrier is not to difficult to jump over
> and run. But It also allow you to explain that if you facilitate the
> apparition of the first "surface" thanks to appropriate method (seeding,
> dust...) you can help the first step (to continue with the barrier story,
> it like you have ladder to help, or the ability to decrease the size of the
> barrier.
>
> For why the crystal and how, I will maybe use the example of orange
> pyramid in the food store. Orange are stable together because they have
> enough contact, because they have relatively homogeneous shape. If you
> mixed orange with water melon it's difficult to obtain nice pyramid.
>
> For crystallization experiment which work, I have no Idea out of the one
> you already mentioned.
>
>
> Hope this help.
>
> Nicolas
>
> Nicolas Foos
> PhD
> Structural Biology Group
> European Synchrotron Radiation Facility (E.S.R.F)
> 71, avenue des Martyrs
> CS 40220
> 38043 GRENOBLE Cedex 9+33 (0)6 76 88 14 87 <+33%206%2076%2088%2014%2087>+33 
> (0)4 76 88 45 19 <+33%204%2076%2088%2045%2019>
>
> On 30/12/2016 11:06, Radisky, Evette S., Ph.D. wrote:
>
> Can anyone point to some especially useful resources to help explain to
> kids (pre-chemistry, ~age 10-12) how and why molecules crystallize? Maybe a
> good online movie or animation?  I am especially needing help with the
> concept of nucleation, and why nucleation is slower and then crystal growth
> faster once nuclei have formed.  I have been supervising some experiments
> growing sucrose crystals from supersaturated solutions, which have worked
> really well, but I am having more difficulty in explaining the underlying
> fundamental concepts in a way that is understandable to the kids.
>
> Thanks!
> Evette
>
> Evette Radisky, PhD
>
> Associate Professor of Cancer Biology
>
> Mayo Clinic Cancer Center
>
> Griffin Cancer Research Building
>
> 4500 San Pablo Road
>
> Jacksonville, FL 32224
>
> tel: 904-953-6372
>
> fax: 904-953-0277
>
>
>


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] Slightly OT: crystallization teaching resources for kids

[Nicolas FOOS]

Dear Evette,

If I was is your situation (explaining nucleation and other concept). I 
will discuss in terms of energy.


I mean obtaining the initial nuclei is the "costly" step in terms of 
energy. To represent that, out the classical curve of energy, I will use 
a metaphoric representation such as jump over a barrier and run after.


With this analogy, it's possible to explain that the first step is 
difficult and the second more accessible. If the barrier is to high, 
it's impossible to continue and run. If you don't have any barrier it's 
easy to run and if you only have a small barrier is not to difficult to 
jump over and run. But It also allow you to explain that if you 
facilitate the apparition of the first "surface" thanks to appropriate 
method (seeding, dust...) you can help the first step (to continue with 
the barrier story, it like you have ladder to help, or the ability to 
decrease the size of the barrier.


For why the crystal and how, I will maybe use the example of orange 
pyramid in the food store. Orange are stable together because they have 
enough contact, because they have relatively homogeneous shape. If you 
mixed orange with water melon it's difficult to obtain nice pyramid.


For crystallization experiment which work, I have no Idea out of the one 
you already mentioned.



Hope this help.

Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 30/12/2016 11:06, Radisky, Evette S., Ph.D. wrote:
Can anyone point to some especially useful resources to help explain 
to kids (pre-chemistry, ~age 10-12) how and why molecules crystallize? 
Maybe a good online movie or animation?  I am especially needing help 
with the concept of nucleation, and why nucleation is slower and then 
crystal growth faster once nuclei have formed.  I have been 
supervising some experiments growing sucrose crystals from 
supersaturated solutions, which have worked really well, but I am 
having more difficulty in explaining the underlying fundamental 
concepts in a way that is understandable to the kids.


Thanks!
Evette

Evette Radisky, PhD

Associate Professor of Cancer Biology

Mayo Clinic Cancer Center

Griffin Cancer Research Building

4500 San Pablo Road 

Jacksonville, FL 32224 

tel: 904-953-6372 

fax: 904-953-0277 

Re: [ccp4bb] Visualize symmetry operations

[chemocev marker]

Hi Aaron
may be this tool can be helpful
https://symd.nci.nih.gov/
or
in the pymol there is script


https://pymolwiki.org/index.php/Symmetry_Axis

Visualizing the transformation between two selections/objects

https://pymolwiki.org/index.php/RotationAxis

PDB has a symmetry browser

http://www.rcsb.org/pdb/staticHelp.do?p=help/advancedsearch/proteinSymmetryBrowser.html

may be it will be helpful

best

Jiri



On Wed, Jan 4, 2017 at 5:20 PM, Aaron Finke  wrote:

> Dear CCP4-keteers,
>
> Is there a program that can visualize symmetry operation positions (e.g.
> twofold screws, fourfolds) in protein structures, like CCDC Mercury does
> for small molecules?
>
> Thanks in advance,
> Aaron
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
>

[ccp4bb] Visualize symmetry operations

[Aaron Finke]

Dear CCP4-keteers,

Is there a program that can visualize symmetry operation positions (e.g. 
twofold screws, fourfolds) in protein structures, like CCDC Mercury does for 
small molecules?

Thanks in advance,
Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

Re: [ccp4bb] Cryo-EM beamline scientist position at CBI, Strasbourg

[Bruno KLAHOLZ]

Dear all,



kind reminder for the cryo-EM beamline position at the Centre for Integrative 
Biology.

Application deadline is next week 15.1.



Best regards,


Bruno Klaholz





De : Bruno KLAHOLZ
Envoyé : vendredi 9 décembre 2016 17:51
À : CCP4BB@JISCMAIL.AC.UK
Objet : Cryo-EM beamline scientist position at CBI, Strasbourg


Dear all,

here is an announcement for a cryo-EM beamline scientist position at the Centre 
for Integrative Biology, Strasbourg, France.

With best regards,

Bruno Klaholz



Cryo-EM beamline scientist position:
The IGBMC/CBI is seeking a experienced scientist to run the cutting-edge EM 
facilities at the Centre for Integrative Biology (CBI) at IGBMC, 
Illkirch/Strasbourg, France.

The CBI provides a leading-edge scientific and technological environment in 
integrated structural biology to address the structure and function of 
biological systems, notably on gene expression, from the atomic, molecular to 
the tissue scales. The CBI http://www.igbmc.fr/grandesstructures/cbi/, hosts 
the French and European Infrastructures for Integrated Structural Biology, 
FRISBI http://frisbi.eu/  and Instruct https://www.structuralbiology.eu/  which 
comprises advanced electron microscopy facilities equipped with cutting-edge 
instrumentation such as Titan Krios and Polara cryo electron microscopes, cryo 
Focused Ion Beam Scanning Electron Microscope (FIB/SEM) and super-resolution 
fluorescence microscopy. The Titan Krios microscope is equipped with Cs 
corrector, Falcon 2 camera, GIF energy filter, K2 camera and phase plate. In 
addition, the EM facility has a suite of associated equipments for sample 
preparation and dedicated computing resources for image processing and 3D 
reconstruction by single particle cryo-EM and cryo electron tomography 
(cryo-ET). For projects and publications of the associated teams see 
http://igbmc.fr/research/department/3/

Applications should be sent via email to 
klah...@igbmc.fr including CV, list of publications, 
names of 3 referees and motivation letter by 15.1.2017.






###
Bruno P. Klaholz
Centre for Integrative Biology
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 964
1, rue Laurent Fries
BP 10142
67404 ILLKIRCH CEDEX
FRANCE
Tel. from abroad: 0033.369.48.52.78
Tel. inside France: 03.69.48.52.78
websites:
http://igbmc.fr/Klaholz
http://www.igbmc.fr/grandesstructures/cbi/
http://frisbi.eu