Posts in Core Rigor and Reproducibility (CoRRe)

Don't miss:

Sunday, March 24th, 6:30 - 7:30pm
Henry B. González Convention Center, Room 214D
The Antibody Crisis: Leveraging machine learning for evidence-based antibody
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Monday, March 25, 4:30 - 5:30  Room 214ABC
Rigor and Reproducibility Practices in a Core Setting
Featuring:
Kevin Knudston, Susan Meyn, Ian Sullivan, Stephen Uebel

Hi,

Below is a link to a webinar (sponsored by the ABRF) presented by University of
Colorado BioFrontiers Institute on how they work with core facilities to bring
computing best practices into their workflows.

https://us1.campaign-archive.com/?u=0ee9670bb3fd42d46d0fa9631&id=6357d87312&e=9ac8f44798

Thanks,

Kevin
--
Kevin L. Knudtson, Ph.D.
University of Iowa
Director, IIHG Genomics Division
116B EMRB
Iowa City, IA  52242



Glad to know this is of interest to you too Laura.

You can link to each chapter meeting at the bottom of the ABRF website.
https://abrf.org/

The on in Atlanta (SEASR 2018) is focusing on R&R too and is at the end of
June.

http://seasr.abrf.org/

The one the fall do not have themes yet.



-----Original Message-----
From: "Core Rigor and Reproducibility (CoRRe)" <email obscured>> on behalf
of Laura Bover <email obscured>>
Reply-To: <email obscured>>
Date: Tuesday, May 29, 2018 at 12:56 PM
To: <email obscured>" <email obscured>>
Cc: Laura Bover <email obscured>>
Subject: Re: [core rigor and reproducibility (corre)] Guidelines for antibody
validation in research settings

    Citing you Frances,
    “I wish I had the time as I think a nice summary of efforts around this
topic, ideally finding common points of action, would be a nice JBT article.  I
also dream of working with other ABRFers to help push this culture shift
forward.  So much to do. So little time.”

    I wish the same. And I can try hard to find the time. May be dividing the
duties, the job can be done.
    Count on me if you find your minutes.
    Thanks!
    Laura
    BTW, I was trying to accommodate my schedule to attend the MADSSC 2018
meeting but I cannot move things around. I don’t find the mail you sent me
about another conference in Atlanta that will talk about the Rigor. Don’t even
remember the date to see if I can attend that one.
    Could you please send it again?
    Thanks!

    Laura Bover, PhD
    Professor
    Director Monoclonal Antibody Core Facility
    University of Texas M.D.Anderson Cancer Center
    Associate member of The University of Texas Graduate School of Biomedical
Sciences at Houston
    Immunology Department/ Genomics Medicine Department
    7455 Fannin St Room 1SCR4.3015/ 1901 East Rd- Room 4SCR5.1039
    Houston- TX 77054
    T 713-563-2281/ 713-563-3301
    F 713-563-3276
    <email obscured>
<email obscured>>


    On 5/3/18, 10:59 AM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Frances Weis-Garcia" <email obscured> on behalf of
<email obscured>> wrote:

        For those interested on this topic ...

        I came across a paper by EuroMAbNet
(https://www.euromabnet.com/about-us/) describing guidelines for validating
antibodies.

        Guidelines Website:
        https://www.euromabnet.com/guidelines/index.php

        Guidelines Manuscript:
        https://www.ncbi.nlm.nih.gov/pubmed/26418356

        Pos/Neg Controls Website:
        https://www.euromabnet.com/guidelines/positive-negative-controls.php

        Additional Articles about Ab Validation on their website:
https://www.euromabnet.com/guidelines/articles-about-antibody-validation.php

        I wish I had the time as I think a nice summary of efforts around this
topic, ideally finding common points of action, would be a nice JBT article.  I
also dream of working with other ABRFers to help push this culture shift
forward.  So much to do. So little time.

        ――
        View topic http://list.abrf.org/r/topic/5dDocqgZV31zHKnxcs4H3n
        Leave group <email obscured>?Subject=Unsubscribe



    The information contained in this e-mail message may be privileged,
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For those who cannot make the June 18-20 MADSSCi, SEASR is also focusing their
meeting this spring on Rigor and Reproducibility, June 27-29, 2018 in Atlanta:

http://seasr.abrf.org/

Yes, I will be interested. I need to see the program.
I will also try to go but this is more difficult yet.
I have to go back to the lab and reorganize calendar.
Thanks Frances.

Laura Bover, PhD
Professor
Director Monoclonal Antibody Core Facility
University of Texas M.D.Anderson Cancer Center
Associate member of The University of Texas Graduate School of Biomedical
Sciences at Houston
Immunology Department/ Genomics Medicine Department
7455 Fannin St Room 1SCR4.3015/ 1901 East Rd- Room 4SCR5.1039
Houston- TX 77054
T 713-563-2281/ 713-563-3301
F 713-563-3276
<email obscured>
<email obscured>>


On 5/1/18, 12:47 PM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Weis-Garcia, Frances/Sloan Kettering Institute" <email obscured> on behalf
of <email obscured>> wrote:

    Doubt they will be recorded, but those going can pick out one or 2 that we
can likely repeat on a webcast.  Any in which you are particularly interested?

    F

    -----Original Message-----
    From: "Core Rigor and Reproducibility (CoRRe)" <email obscured>> on
behalf of Laura Bover <email obscured>>
    Reply-To: <email obscured>>
    Date: Tuesday, May 1, 2018 at 9:11 AM
    To: <email obscured>" <email obscured>>
    Subject: Re: [core rigor and reproducibility (corre)] Rigor and
Reproducibility at MADSSCi in June

        Thanks for the info. It is a really important topic. Though, like
Frances said, I am not sure that I can attend. Will it be possible to record
the sessions and discussions or webcast?
        Thanks


        Laura Bover, PhD
        Professor
        Director Monoclonal Antibody Core Facility
        University of Texas M.D.Anderson Cancer Center
        Associate member of The University of Texas Graduate School of
Biomedical Sciences at Houston
        Immunology Department/ Genomics Medicine Department
        7455 Fannin St<x-apple-data-detectors://17/1> Room 1SCR4.3015/ 1901
East Rd- Room<x-apple-data-detectors://18>4SCR5.1039
        Houston- TX 77054<x-apple-data-detectors://19/0>
        T 713-563-2281<tel:713-563-2281>/ 713-563-3301<tel:713-563-3301>
        F 713-563-3276<tel:713-563-3276>
<email obscured><email obscured>>

        Sent from my iPhone

        On May 1, 2018, at 9:16 AM, Weis-Garcia, Frances/Sloan Kettering
Institute
<email obscured><email obscured>>>
wrote:

        Thanks for bringing this to our attention.

        Sorry I cannot be there ... to much travel going on this spring / early
summer.  Would love to know how it goes.

        Frances

        -----Original Message-----
        From: "Core Rigor and Reproducibility (CoRRe)"
<email obscured><email obscured>>> on behalf of ncfisher
<email obscured><email obscured>>>
        Reply-To: <email obscured><email obscured>>>
        Date: Tuesday, May 1, 2018 at 8:04 AM
        To: <email obscured><email obscured>>>
        Subject: [core rigor and reproducibility (corre)] Rigor and
Reproducibility at MADSSCi in June

           This year, the MADSSCi meeting in Baltimore will be dedicated to
Rigor and Reproducibility.

           http://madssci.abrf.org/

           Cores: At the Forefront of Rigor and Reproducibility

           MAD SSCi 2018 Baltimore, MD - June 18-20, 2018
           hosted by the Johns Hopkins University School of Medicine
           Turner Building Concourse, 720 Rutland Avenue


           ――
           View topic http://list.abrf.org/r/topic/3WaDbHyjr6Itqt7U34559u
           Leave group <email obscured>?Subject=Unsubscribe

        ――
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from your systems.

Thanks for the info. It is a really important topic. Though, like Frances said,
I am not sure that I can attend. Will it be possible to record the sessions and
discussions or webcast?
Thanks


Laura Bover, PhD
Professor
Director Monoclonal Antibody Core Facility
University of Texas M.D.Anderson Cancer Center
Associate member of The University of Texas Graduate School of Biomedical
Sciences at Houston
Immunology Department/ Genomics Medicine Department
7455 Fannin St<x-apple-data-detectors://17/1> Room 1SCR4.3015/ 1901 East Rd-
Room<x-apple-data-detectors://18>4SCR5.1039
Houston- TX 77054<x-apple-data-detectors://19/0>
T 713-563-2281<tel:713-563-2281>/ 713-563-3301<tel:713-563-3301>
F 713-563-3276<tel:713-563-3276>
<email obscured><email obscured>>

Sent from my iPhone

On May 1, 2018, at 9:16 AM, Weis-Garcia, Frances/Sloan Kettering Institute
<email obscured><email obscured>>>
wrote:

Thanks for bringing this to our attention.

Sorry I cannot be there ... to much travel going on this spring / early summer.
Would love to know how it goes.

Frances

-----Original Message-----
From: "Core Rigor and Reproducibility (CoRRe)"
<email obscured><email obscured>>> on behalf of ncfisher
<email obscured><email obscured>>>
Reply-To: <email obscured><email obscured>>>
Date: Tuesday, May 1, 2018 at 8:04 AM
To: <email obscured><email obscured>>>
Subject: [core rigor and reproducibility (corre)] Rigor and Reproducibility at
MADSSCi in June

   This year, the MADSSCi meeting in Baltimore will be dedicated to Rigor and
Reproducibility.

   http://madssci.abrf.org/

   Cores: At the Forefront of Rigor and Reproducibility

   MAD SSCi 2018 Baltimore, MD - June 18-20, 2018
   hosted by the Johns Hopkins University School of Medicine
   Turner Building Concourse, 720 Rutland Avenue


   ――
   View topic http://list.abrf.org/r/topic/3WaDbHyjr6Itqt7U34559u
   Leave group <email obscured>?Subject=Unsubscribe

――
View topic http://list.abrf.org/r/topic/3ZhXRGsC24hwHVLCZdamOZ
Leave group <email obscured>?Subject=Unsubscribe



The information contained in this e-mail message may be privileged,
confidential, and/or protected from disclosure. This e-mail message may contain
protected health information (PHI); dissemination of PHI should comply with
applicable federal and state laws. If you are not the intended recipient, or an
authorized representative of the intended recipient, any further review,
disclosure, use, dissemination, distribution, or copying of this message or any
attachment (or the information contained therein) is strictly prohibited. If
you think that you have received this e-mail message in error, please notify
the sender by return e-mail and delete all references to it and its contents
from your systems.

This year, the MADSSCi meeting in Baltimore will be dedicated to Rigor and
Reproducibility.

http://madssci.abrf.org/

Cores: At the Forefront of Rigor and Reproducibility

MAD SSCi 2018 Baltimore, MD - June 18-20, 2018
hosted by the Johns Hopkins University School of Medicine
Turner Building Concourse, 720 Rutland Avenue

Hi,

I was recently working with an investigator on trouble shooting their ChIP-Seq
experiment that apparently had “stopped working”.  They insisted nothing had
changed.  During the discussion they indicated that they had “even purchased a
brand new Ab” against the target they were pulling down.  After hearing this,
some of the horror stories about Ab specificity that were shared at the ABRF
2017 annual meeting suddenly came to mind.  I suggested to the investigator
that he may want to confirm the specificity and working titer of this “new”
antibody. He did a titration experiment and found that the experiment was now
“working again” if he used a higher titer of the Ab for the pull down.

As noted above, we also discussed Ab validation.  I pointed out an article by
Natan Blow on page 51 of the August Issue of BioTechniques. He noted that “many
articles have been written about the problem of antibody validation, but far
fewer have focused on the solutions.  In the article, there is reference to a
scoring system that was develop by the GBSI that could be used to evaluate Abs.
There was also a reference to David Rimm (2010)  that illustrated a proposed
validation flowchart.

I shared these validation workflows with the investigator and he indicated that
he would not likely follow through the validation workflows suggested by this
article.   He expects the provider of the Ab to have already done the
validation.

I am curious to know if other cores have had similar experiences when working
with investigators who are using Abs to prepare samples for use in your
facility.  Minimally, what are you advising your users to do when working with
Abs?

Thanks,

Kevin
--
Kevin L. Knudtson, Ph.D.
University of Iowa
Director, IIHG Genomics Division
323 EMRB
Iowa City, IA  52242

TEL: 319-335-7251
FAX: 319-335-6737
E-mail: <email obscured><email obscured>>

Dear All,
This is a test of the response function

Henriette
CCoRRe member
University of Michigan