Results tagged “workshop” from The SIBYLS Beamline

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Date: October 2 - 3, 2019 Location: Building 33 at Lawrence Berkeley National Laboratory, Berkeley, CA

Building / ROOM : 33-306

This two-day workshop will cover frontiers in biological SAXS and will provide participants with software tutorial sessions for biological SAXS in addition to hands-on training in experimental techniques. The latest advances in SAXS studies on biological systems will be discussed with a particular focus on dynamic and flexible structures in biomolecules, membrane protein scattering, and complementary methods in crystals and in solution. Updates on current developments of software for SAXS analysis and solution structure modeling will be illustrated.

The first day of the workshop will begin with a brief run-through on current updates. Greg Hura and Michal Hammel, Berkeley Lab’s SAXS beamline scientists, will introduce the capabilities of the mail-in program at SIBYLS and the future of high-throughput and SEC-SAXSat the SIBYLS Beamline. Distinguished speakers will contribute to the basis of the workshop over the two days by sharing complementary experimental approaches and modeling techniques. This will provide for a flux of ideas among workshop participants and inspire new perspectives for future data analysis. The second day will be dedicated to practical hands-on exercises with experts in SAXS software for data processing (SCATTER, FrameSlice and RAW, SAXS similarity maps, modeling tools (FOXS - MultiFoXS, BILBOMD and SAXS shape calculator).

Enrollment is limited to 30 participants. 





Inquires: Kathryn Burnett

Registration: Registration is now open. To attend the workshop you need to REGISTER for the 2019 ALS user meeting. When you register, indicate that you plan to attend the “10th Annual SIBYLS bioSAXS Workshop”.

SCHEDULE : October 2nd, 2019

Building / ROOM : 33-306

Day 1: BioSAXS Workflow

8:30-8:40 Introduction to the SIBYLS team and Workshop Agenda (Hammel)

8:40 - 9:20 Key Note - Mark Glover (Uni. Alberta) Building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time

9:20 - 10 SAXS basics (G. Hura)

10 - 10:20 Break

10:20 - 12:20pm HT-SAXS, details of collection, getting intensity vs q (Burnett and Hura)

12:20 - 1:30 Lunch

1:30 - 2:30 SEC-SAXS-MALS, details of collection, getting intensity vs q (Hammel and Rosenberg)

2:30 - 3:00 ALS and beamline tour (SIBYLS team)

3:00 - 3:30 Analysis of SEC-SAXS-MALS (Hammel)

3:30- 3:50 Break

3:50 - 4:10 Ben Horst ( UC Berkeley) Allosteric activation of the NO receptor soluble guanylate cyclase revealed by cryo-EM and SAXS

4:10 - 4:30 Lauren Carter (University of Washington) De novo protein design validated by SAXS

4:30 - 4:45 Soumya Remesh (NCI) Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling

4:45 - 5 Curtis Hodge (LBNL) Functionalized Nanocage for Antibody Display

October 3rd, 2019 Day 2: Beyond Shapes with SAXS

8:30 - 9:15 HT-SAXS examples (Hura)

9:20 - 10 Special SEC-SAXS-MALS tools with RAW and Evolving SVD (Hammel)

10 - 10:20 Break

10:20 - 12:20pm User posed problem

12:20 - 1:30 Lunch

1:30 -2:00 SAXS modeling, BILBOMD, FoXS etc… (Hammel)

2:00-5:00 Hands on practical

Date: May 9th 2019

Location: Advanced Light Source at Lawrence Berkeley National Laboratory, Berkeley, CA

Building 6, conference room #2202

SAXS_board.JPG This one-day workshop for current and future SIBYLS users will provide participants with software tutorial sessions for biological SAXS. The latest advances in SAXS studies on biological systems will be discussed with particular focus on advances in synchrotron scattering techniques, modeling of dynamic and flexible structures, and integrating bioSAXS analysis within high resolution structures.
Updates on current developments of software for SAXS analysis pertaining to structural biology will be reviewed.

We will begin with a brief run-through on current updates. Greg Hura, Berkeley Lab’s SAXS Beamline Scientist will introduce the future of high throughput. Michal Hammel, another one of Berkeley Lab’s SAXS Beamline Scientists, will present current developments in size exclusion chromatography coupled SAXS (SEC-SAXS) and give a talk about integrating high-resolution models in the SAXS modeling. Students and postdocs are encouraged to bring their own SAXS data collected at SIBYLS. We will provide an opportunity for participants to present and discuss their projects with the group. If you are interested in discussing your SAXS project, please email Kathryn Burnett. This will provide for a flux of ideas among workshop participants, and inspire new perspectives for future data analysis. During the afternoon session we will provide practical hands-on exercises with experts in SAXS software for data processing (SCATTER, FrameSlice and RAW, SAXS similarity maps, modeling tools (FOXS - MultiFoXS, BILBOMD and SAXS shape calculator).

Organizers: SIBYLS



Inquires: Kathryn Burnett

Limited to 30 participants.

Registration: Registration is now open. To attend the workshop you need to send an email to Kathryn Burnett

Lunch is provided.

SCHEDULE :

May 9, 2019 12:00 pm - 5:00 pm

Building 6, conference room #2202

12:00 - 1:30 pm Greg Hura and Michal Hammel Working lunch and introductions

1:30 - 2:30 pm Greg Hura and Michal Hammel Tour of the ALS, both SAXS and MX end stations

2:30 - 3:00 pm Scott Classen “Crystallographic Options at the ALS”

3:00 - 3:40 pm Michal Hammel and Daniel Rosenberg “Size Exclusion Coupled SAXS issues”

3:40 - 4:20 pm Greg Hura and Kathryn Burnett “High-throughput SAXS issues”

4:20 - 5:00 pm Hands on User Projects

**figintro.jpg Date: October 3 - 4, 2018 Location: Advanced Light Source at Lawrence Berkeley National Laboratory, Berkeley, CA

Building 33 room 306

The two-day workshop, held during ALS user meeting, will provide participants with software tutorial sessions for biological SAXS in addition to hands-on training in experimental techniques. The latest advances in SAXS studies on biological systems will be discussed with particular focus on advances in synchrotron scattering techniques, modeling of dynamic and flexible structures, bioSAXS with membrane protein, and integrating bioSAXS analysis within cryo-EM imaging.
Updates on current developments of software for SAXS analysis pertaining to structural biology will be reviewed.

The first day of the SIBYLS annual workshop will focus on applied science while the second day will focus more on practical tutorials.

We will begin with a brief run-through on current updates. Greg Hura, Berkeley Lab’s SAXS Beamline Scientist will introduce the future of high throughput. Three keynote speakers: Walter Chazin (Vanderbilt), Thomas Weiss (SLAC, Stanford) and Steve Meisburger (Princeton), will continue Dr. Hura’s discussion by elaborating on the basics of SAXS and the fascinating integration of bioSAXS in integrative structural biology. Michal Hammel, another one of Berkeley Lab’s SAXS Beamline Scientists, will present current developments in size exclusion chromatography coupled SAXS (SEC-SAXS) and give a talk about integrating high-resolution models in the SAXS modeling. Other distinguished speakers from the SIBYLS user community: Chris Brosey (MD Anderson) , Fatma Zehra Yildiz (Harvard) and George Ueda (University of Washington) will contribute to the basis of the workshop over the two days by sharing complementary experimental approaches and modeling techniques. Screen Shot 2018-07-19 at 2.35.35 PM.png

For the second day, students and postdocs are encouraged to bring their own SAXS data collected at SIBYLS. During the morning session, we will provide an opportunity for participants to present and discuss their projects with the group. If you are interested in presenting, please email Kathryn Burnett. This will provide for a flux of ideas among workshop participants, and inspire new perspectives for future data analysis.

The afternoon session will be dedicated to practical hands-on exercises with experts in SAXS software for data processing (SCATTER, FrameSlice and RAW, SAXS similarity maps, modeling tools (FOXS - MultiFoXS, BILBOMD and SAXS shape calculator).

Enrollment is limited to 30 participants. 



Organizers: Michal Hammel, Greg Hura



Inquires: Kathryn Burnett

Registration: Registration is now open. To attend the workshop you need to REGISTER for the 2018 ALS user meeting. When you register, indicate that you plan to attend the “9th Annual SIBYLS bioSAXS Workshop”.

SCHEDULE :

October 3rd, 2018 Building 33 room 306

8:45 am Michal Hammel and Greg Hura “Welcoming remarks”

9:00 am Greg Hura (LBL) “Redefining frontier in bioSAXS”

10:00 am Break

10:20 am Walter Chazin (Vanderbilt) “Redefining of protein dynamicity by integrating NMR and SAXS”

11:00 am Steve Meisburger (Princeton) “Redefining of bioSAXS by the SEC-SAXS approach and SVD deconvolution”

11:40 am Michal Hammel (LBL) “Integrative structural modeling by combining crystallography, SAXS and X-ray tomography”

12:00 pm Lunch and Exhibitors—ALS Patio and Exhibitor Tent

1:30 pm Beamline tour and demonstration, Greg Hura and Daniel Rosenberg, LBNL

2:20 pm Thomas Weiss ( SLAC) “Overview on the workflows and how we do SAXS at SSRL”

3:00 pm Break

3:20 pm Chris Brosey (MD Anderson) “Using High-Throughput SAXS to Illuminate Allosteric Landscapes and Advance Drug Discovery”

3:50 pm Fatma Zehra Yildiz (Harvard) “TBD”

4:20 pm George Ueda (Washington Uni) “Computational design of self-assembling cyclic protein homo-oligomers”

4:40 pm Soumya Remesh (LBL) “HU multimerization shift controls nucleoid compaction as seen through SAXS and X-ray tomography”

5:00 pm Gather for Evening Session—Building 50 Auditorium

October 4th, 2018

9:00 am Short students presentations followed by an open discussion

10:00 am Break

10:15 am Greg Hura: “SAXS analysis part 1”

11:15 am Michal Hammel: “SEC-SAXS data processing and SVD deconvolution”

12:00 am Lunch and Exhibitors—ALS Patio and Exhibitor Tent

1:00 pm Greg Hura, “SAXS Analysis part 2”

1:30 pm Michal Hammel “Tools for modeling flexibility in proteins using SAXS data”

2:00 pm Greg Hura “SAXS Similarity Maps”

2:20 pm Practical session with Mentors

5:00 pm Closing comments: Michal Hammel and Greg Hura

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