The APS shut down on April 17, 2023 for an upgrade. During this APS-U dark period the BioCAT beamline is unavailable for x-ray experiments. We anticipate resuming user experiments in late 2024/early 2025.
Find out more about: the APS-U; SAXS experiments during the APS-U dark period; Fiber experiments during the APS-U dark period.
Contents
Overview
BioCAT is an NIH-supported Biotechnology Research Resource. Anyone can use the facility for free by putting in an application through the APS GUP program. These applications are reviewed on the basis of feasibility and scientific merit. Obtaining time at the BioCAT facility is a multiple-step process. Below is a listing of the things you need to do - from start to finish - to acquire, use, and complete time at BioCAT. Please also check the APS new user checklist.
Discuss Your Proposed Experiment with Us
Our facility is very flexible and can accommodate most experiments that fall within our supported techniques. We strongly encourage you to discuss your experiment with the user liaison for your technique. This will save a lot of time assembling and debugging your set-up giving you more time to acquire high-quality data once you’ve arrived.
Register as an APS Experimenter (“User”)
The Advanced Photon Source resides within Argonne National Laboratory which is a controlled-access facility. This step initiates the process for granting access to ANL, as well as the process for ensuring that safety and compliance requirements are met.
Everyone participating in the experiment (mailing samples or coming on site) must be a registered user. New users should register and existing users should check to make sure their site access is still valid. It can take the APS several weeks to process your user registration, both for new users and for updates to current users’ site access, so make sure everyone in your group does this as soon as you know you want beamtime.
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The primary mechanism for access to BioCAT is through the APS General User Program. Further information on classes of experiments, allocation of time by category, and the proposal review process is available from the APS.
If you are apply for beamtime within the current run, or for the next run after the standard GUP proposal deadline has passed, you will need to put in a Rapid Access proposal. To do so, when creating a new proposal select the “General Users” proposal and then select the “Rapid Access General User Proposal (DO NOT USE FOR MC PROPOSALS)” for your General User (GU) Proposal Type. These proposals are good for only one run.
Users with active proposals wishing time in the next run should submit a beamtime request by following the directions for a Returning Proposer on the APS website. Users with an active proposal who want time in the current run, or for the next run after the standard GUP proposal deadline has passed can put in a rapid access beamtime request.
For all proposals to BioCAT you must list the BioCAT beamline, “18-ID-D”, as one of the three beamlines in the “Choice of Beamline” section in the Beamtime Request. For a Rapid Access proposal, you should list only BioCAT in this section.
Complete the Experiment Safety Assessment Form (ESAF)
Every proposal awarded beam time must be accompanied by an approved Experiment Safety Assessment Form (ESAF) before it is allowed to proceed.
An ESAF for an on-site experiment must be submitted at least 14 days before the experiment or it will not be approved. An ESAF for a remote/mail-in experiment must be submitted at least 7 days before the experiment or it will not be approved. We recommend submission before these hard deadlines so any issues can be resolved and your experiment can proceed as planned. Please visit our ESAF and safety and compliance pages for more information.
For an ESAF to be valid, it must list all experimenters to be present at the facility or mailing in samples. ESAFS will not be approved if listed experimenters do not have valid site access, so you must register as a user/renew your site access as above. In addition, when listing materials, samples names must be written out in full and (when appropriate) the expression system must be included. You should not use abbreviations with the exception of “DNA” and “RNA”, and sample names should be written as, e.g., “Lysozyme from Chicken Egg White” rather than “Sample 1”.
If your ESAF involves any of the additional hazards listed below it will require a more detailed (and, therefore, prolonged) review before access can be granted, so you should submit it at least 1 month before your experiment:
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Experiments utilizing any of the following items will have to be coordinated far in advance with your Scientific Contact, Mark Vukonich (BioCAT BSO), and Nena Moonier (APS BSO) to be reviewed formally by the ANL Institutional Biosafety Committee(IBC) as well as the IIT IBC:
- Human tissues or fluids
- Animal tissues derived from diseased animals
- Some plants and plant pathogens
- Some viruses and bacteria
- Some proteins which may be involved in causing disease or harmful effects of the disease process
- Some sequences of DNA or RNA
The IBCs oversee the safety of all experimental participants and ratify the proposed experimental protocol according to Centers for Disease Control, Department of Transportation, and Department of Agriculture regulations. This is a process which can take upwards of three months; so consult with your Scientific Contact for IBC application instructions well in advance if you think your experiment might require the approval of the IBC.
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Use of any other than a class I laser requires additional ANL-supplied training. You will need to schedule a few hours to complete this training. In addition, use of a class IIIb or IV laser will require a written Standard Operating Procedure (SOP) and an on-site review of the assembled (but not aligned) laser system before work may begin. A class IV laser will require all operators to have an ANL-approved off-site eye examination.
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All electrical equipment which is not certified by a Nationally Recognized Testing Laboratory (NRTL) (such as Underwriters Laboratories) or is modified will need to be inspected before it may be used at the APS. A listing of approved NRTLs is provided here.
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The preferred method of shipping at Argonne is FedEx Priority Overnight. If you want your samples to arrive promptly (the morning after shipping), you must use this method. Otherwise they may arrive in the afternoon, or even later. Our shipping page has more details and our shipping address. Note that BioCAT cannot receive packages on weekends or holidays.
Please be aware that the transportation of many materials is regulated by the US Department of Transportation as well as ANL. Failure to comply with DOT regulations can result in heavy fines. Failure to comply with ANL regulations can result in loss of access to the facility.
Establish a “User Account” - BSL2 experiments only
BioCAT requests that all experimenters doing BSL2 experiments submit a purchase order to ANL in care of the APS “User Account Specialist” to provide a mechanism for covering costs that may be incurred at the APS on their behalf. Such costs include: shipping, purchases from the APS stock room, supplies ordered through the Argonne Materials Ordering System (AMOS), and fabrication of items at an APS/ANL shop.
Complete Training and Orientation
Once you arrive, both the APS and BioCAT will require certain training and orientation sessions to be taken before you may proceed with your experiment. These sessions will be determined by the ESAF process. Some of these are available on-line. Please visit Safety and Compliance for further details.
Arrive at the Beamline
Argonne National Lab is a closed campus. In order to obtain site access you must first register (step 2, above). Any on-site user arriving outside of normal business hours on a weekday or on a holiday or weekend must request a Gate Pass in advance of their arrival or they will not be allowed on site. Current information on business hours and how far in advance a gate pass must be requested is available here: https://aps.anl.gov/Users-Information/Updates/Covid-Rule-Regulations.
For on-site users, please note that in order to get your user photo badge or gate pass, you will have to show a valid form of photo identification. If you want to use a driver’s license or other state identification card as your photo ID it must be REAL-ID compatible. The APS website has more information on how to obtain site access.
Nominally your beamtime starts at 8 am on your first scheduled day. In practice, you should usually plan to arrive at the beamline between 9:30-10 am unless otherwise specified by your scientific contact. If you have particular questions or concerns about the start of your beamtime, contact your scientific contact. You cannot start any work until you ESAF is posted, so if you arrive before your scientific contact wait at the beamline or in the LOM until they arrive. Do not start working on your own!
Observe Beamline Etiquette
Please, while you’re here:
Be courteous to your host staff.
We work hard supporting back-to-back experiments that run 24 hours a day for multiple days during the three-month-long “run”. We will do everything we can to support your experiment while you’re here, but we will also show you basic trouble-shooting algorithms that will help you diagnose some problems on your own—-saving you time.
Be patient.
Your experiment block includes time required for set-up and training. For non-standard experiments, unless otherwise arranged, you should expect at least one shift to be used for basic setup before we’re ready to begin the debugging phase.
Keep your work areas as orderly and free of debris as possible.
Relinquish the facilities at the appointed time.
Typically, the experimenter following you begins at 0800 on your last day. Unless otherwise arranged, you should have your equipment already dismantled and the hutch and bio-chem lab cleared by this time.
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It is now common for experiments to generate tens of GB (or more) of data. Please be prepared to collect this data so that you can transmit it to your home institution.
For on-site users we recommend a USB 3 external hard-drive with (a minimum of) 1 TB of space. BioCAT does not supply experimenters with storage media.
For mail-in users (and upon request for on-site users) BioCAT will upload your data to Globus and provide instructions for downloading your data from there.
Complete an End of Experiment Form
Once your experiment is over, we request that you provide BioCAT and the APS with any comments and constructive criticisms so that your next experiment can run more efficiently.
Refine Your Experiment
Most of our experimenters return for subsequent experiments. Keep in touch with your scientific contact and follow through on proposed modifications to your experiment. It is very important that ideas for improving your experiment are not lost between visits.
Publish Your Results
When you publish your results, be sure to properly acknowledge the APS and BioCAT, and notify both the APS and BioCAT of such publications. Peer-reviewed publications are are the primary measure of scientific output. Properly documented publications insure that funds are available to continue operating the facility.
SAXS Specific Information
In the following video from the Everything BioSAXS workshop, BioCAT Deputy Director Jesse Hopkins discusses what you need to know about planning and performing SAXS experiments at BioCAT, including getting beamtime (get slides).