Ask a Biosafety Expert: A new service from DIYbio.org to get some free advice from biosafety experts

[Jason Bobe]

HI All -

After more than a year of piecing it together, I am very happy to say that DIYbio.org launched this morning a new service that aims to provide free biosafety advice to the DIYbio community.  Please check it out:

http://ask.diybio.org/

Carolyn Johnson at the Boston Globe has a very nice write-up:

http://www.boston.com/news/science/blogs/science-in-mind/2013/01/17/safe-dump-this-down-the-drain-ask-biosafety-expert/XjpWRYkgrVcKLMatLPZqTK/blog.html

I really don't know what to expect in terms of how many questions we will receive and how many responses this team of 3 biosafety experts will be able to turn around each month.  So, the service may evolve as learn what the needs are out there.

We solicited a few question from BioCurious to get things started and got three great questions. We hope to have the first set responses up in the next few weeks.  If you've got any questions related to your own activities, please submit those.

Thanks!

Jason Bobe

[Patrik D'haeseleer]

Any idea when we might see some of the first answers coming out? Or how long you expect the typical response time to be?

A huge THANK YOU for this service - this is an outstanding resource!

Patrik

[Nathan McCorkle]

On Thu, Jan 17, 2013 at 8:54 AM, Jason Bobe <jaso...@gmail.com> wrote:
> HI All -
>
> After more than a year of piecing it together, I am very happy to say that
> DIYbio.org launched this morning a new service that aims to provide free
> biosafety advice to the DIYbio community. Please check it out:
> http://ask.diybio.org/

Wouldn't it have been better to just get these folks to sign up for
this mailing list last year? We already have tons of users, activity,
google hits for related questions. The 'Ask' button could have just
simply posted the question to the google group.


--
-Nathan

[Cathal Garvey]

This is *excellent* news, I'm delighted to see it!
Although I'm delighted at the web-interface (I don't feel the mailing list is the answer to everything), it would be nice to have the experts read even the digests of the mailing list from time to time, too. Their expert input would be very welcome on this list!

Jason Bobe

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[Bryan Bishop]

On Fri, Jan 18, 2013 at 3:12 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> google hits for related questions. The 'Ask' button could have just
> simply posted the question to the google group.

I agree. Safety isn't something to tack on. Also, from time to time we
answer biosafety questions on the list, and if our answers are wrong,
people with more training in safety should weigh in and help fix
things. By "should" I mean "it would be friendly of them", not "I
expect other people to make up for any hazardous ideas flying around".

- Bryan
http://heybryan.org/
1 512 203 0507

[Jason Bobe]

On Friday, January 18, 2013 5:40:17 PM UTC-5, Cathal wrote:

This is *excellent* news, I'm delighted to see it!
Although I'm delighted at the web-interface (I don't feel the mailing list is the answer to everything), it would be nice to have the experts read even the digests of the mailing list from time to time, too. Their expert input would be very welcome on this list!

That might be possible at some point if a large enough community of biosafety volunteers is established that would be willing to chime in here or there.  But, I think it is a lot to ask this small group of volunteers to read through a bunch of irrelevant stuff, looking for safety issues!  Sort of like asking my doc to skim my email making to make sure I'm healthy :)

I like the idea of posting questions directly to a mailing list, I could see that being a future scenario worth exploring.  Although, responding to a single, well-specified question is a different beast than engaging in an ongoing discussion.  Also, I could see the submission form getting more structured. Images of workspace may be important to answering some questions.  Typically biosafety officers are collocated with scientists and get the opportunity to see the context etc. 

Jason

[Jason Bobe]

On Friday, January 18, 2013 3:50:21 PM UTC-5, Patrik D'haeseleer wrote:

Any idea when we might see some of the first answers coming out? Or how long you expect the typical response time to be?

Don't know.  Depends on the questions I guess (both volume and complexity).  We're learning by doing here and I'm sure the workflow will evolve as we go!

 

A huge THANK YOU for this service - this is an outstanding resource!

You are welcome!

Jason

[Bryan Bishop]

On Sat, Jan 19, 2013 at 6:44 PM, Jason Bobe wrote:
> Sort of like asking my doc to skim my email making to make sure I'm healthy
> :)

What's wrong with a doctor replying to his patient's emails, besides
liability/insurance? It might not be as absurd as you think.

[Nathan McCorkle]

On Sat, Jan 19, 2013 at 4:44 PM, Jason Bobe <jaso...@gmail.com> wrote:
> Sort of like asking my doc to skim my email making to make sure I'm healthy :)
>
> I like the idea of posting questions directly to a mailing list

Just having the Ask button send the email to the safety folks, but
also to the google group should be an easy add. Then just have the
advisors post their answers to the google group, or re-post them from
diybio.org to the google group in the same thread.

--
-Nathan

[Jason Bobe]

On Saturday, January 19, 2013 8:50:13 PM UTC-5, Bryan Bishop wrote:

On Sat, Jan 19, 2013 at 6:44 PM, Jason Bobe wrote:
> Sort of like asking my doc to skim my email making to make sure I'm healthy
> :)

What's wrong with a doctor replying to his patient's emails, besides
liability/insurance? It might not be as absurd as you think.

Yes, I think there is a difference between asking my doctor to answer an email I send her, compared to asking her to read my whole inbox looking for health issues.  It is obviously not absurd to ask someone to respond to an email.  

Jason 

[Jason Bobe]

Yeah, my plan was to post the responses to the mailing list simultaneously with posting them in an archive at DIYbio.org.  Maybe with a standard subject line prefix, like [DIYbio.org ABE] so they are easy to find.

Jason

[Nathan McCorkle]

On Jan 20, 2013 12:06 PM, "Jason Bobe" <jaso...@gmail.com> wrote:
>
> Yeah, my plan was to post the responses to the mailing list simultaneously with posting them in an archive at DIYbio.org.  Maybe with a standard subject line prefix, like [DIYbio.org ABE] so they are easy to find.
>

Cool, sounds good!

[Mackenzie Cowell]

I am excited about the utility of the ask.diybio.org service.  To encourage transparency and discussion, I think it would be great if the safety questions were posted to the google group in parallel with their submission to the ask.diybio.org service.  Perhaps when Jason reviews submissions periodically, he can judiciously post the ones selected to be answered by the experts to the group from a special google group account.  Then we, as a community, can research and discuss any perceived issues - if desired - while we wait for the expert opinion.  Sounds fun!

It will be interesting to see if there are just a handful of questions each month (or less), or if the service gets hundreds.

Mac

[Michael Atkinson]

Very impressive

[Patrik D'haeseleer]

Cool! First response is up, and it's about the idea of using amphibian or reptilian cell lines on the BioPrinter at BioCurious (for the record, we're not working with *any* animal cells right now):

http://ask.diybio.org/questions/are-there-any-special-safety-issues-to-consider-when-planning-to-work/

Question:

We have a group at BioCurious that wants to print tissues using a bioprinter they have created - a machine that prints cells on a surface like an inkjet printer. They originally wanted to print mammalian tissue cells. We've decided not to allow this at BioC as we would want to treat such work as BSL2 and don't have those facilities (reason being there is no way to certify it is free of all human pathogens or that even if free the cell line would not become contaminated). I suggested to the group that they look at invertebrate cells, they said this was not suitable, but proposed using an amphibian or reptilian cell line. I can't think of why this wouldn't be safe, but as this is so far out of the work I have done I don't feel comfortable making that determination. Do you have any insight on if there are any safety considerations to working with amphibian or reptilian cells?

BioCurious is a community lab in the San Francisco bay area - you can find more about us at http://biocurious.org.

Answer from a Biosafety Officer:

January 28, 2013

Response from Biosafety Advisory:

Work with amphibian or reptilian cells can be conducted safely at BSL-1.  While these types of cells are less likely than mammalian tissue cells to carry human pathogens, if the cells will be isolated in the laboratory, as opposed to being purchased from a vendor, the group should be aware that fungal and bacterial skin infections could occur from contact with reptiles or amphibians (Lewis et al.  Clinical Infectious Diseases 2003; 37: 390-397).  Good work practices such as wearing gloves when working with the cells, especially if group members have broken skin, and washing hands after working with the materials should be followed.  

The group will want to devise a method to decontaminate their bioprinter after use with the cell lines.  An effective disinfectant is a 1:10 dilution of Clorox bleach in water (1 part Clorox household bleach – not scented or splashless versions – to 9 parts water).  The surfaces/items to be decontaminated should remain wet with the 1:10 dilution of bleach for at least 10 minutes to make sure that they have been properly disinfected.  Depending upon the materials used to build the bioprinter, this bleach solution may cause corrosion of metal parts over time if the equipment is not thoroughly rinsed with water.

On Thursday, January 17, 2013 8:54:25 AM UTC-8, Jason Bobe wrote:

[Jason Bobe]

On Wednesday, January 30, 2013 11:36:14 PM UTC-5, Patrik D'haeseleer wrote:

Cool! First response is up, and it's about the idea of using amphibian or reptilian cell lines on the BioPrinter at BioCurious (for the record, we're not working with *any* animal cells right now):

You beat me to it!  Was going to post later today.  Had a formatting bug to work out but now resolved.  The second post should go up tomorrow and i'll post it to the mailing list too.

Jason

[Taylor R.]

This is really cool. One of the largest concerns over DIY Bio is the safety aspect, and that's what the average person worries about when told to conjure up the image of "everyday people" doing lab work in a garage or a basement. This is such a simple concept, but it shows how far DIY Bio has come as a movement in such a short amount of time, and just how much the unspoken policy of sharing has held strong in the community as a whole -- as well as how quickly the community can respond to concerns in an effective way.

[Nathan McCorkle]

GOOGLE TRANSLATION:
"Will you be able to ask questions in languages other than English?,
As the Spanish or French, the most popular at least"

On Sat, Apr 20, 2013 at 11:41 PM, m4xl3s <nicola...@gmail.com> wrote:
> ¿Usted será capaz de hacer preguntas en idiomas distintos del Inglés?, Como
> el español o Franses, los porlomenos más populares

>
>
>
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[Jason Bobe]

On Monday, May 6, 2013 1:48:05 PM UTC-4, Nathan McCorkle wrote:

GOOGLE TRANSLATION:
"Will you be able to ask questions in languages other than English?,
As the Spanish or French, the most popular at least"

Hopefully we will be able to expand the service to other languages, both the ability to pose questions in different languages and to have the knowledgebase translated into different languages.

Jason

[jarlemag]

So...what happened to this?

-JP

[Nathan McCorkle]

On Sun, Jul 21, 2013 at 12:45 PM, jarlemag <jarle...@gmail.com> wrote:
> So...what happened to this?

What do you mean? Looks like the link still works:
http://ask.diybio.org/

[jarlemag]

Yes, but there doesn't seem to be any new answers. I submitted a question when the service first opened, and I imagine I'm not the only one who did and didn't get an answer. If there was lots of questions being answered that wouldn't be so strange, but since no answers have appeared in a long while I'm just wondering if there is any attention being paid to it at all. I don't suppose the panel gets paid, so it shouldn't be surprising it isn't very highly prioritized, but still a bit disappointing that it seems to have been forgotten so quickly.
 

-JP

[jarlemag]

Uhh yeah...I should have 30 points substracted from my IQ score I think. I remember looking at the page a long time ago when there were only a few answers, and checked back now to see the same page...and completely failed to nice the "see more" link. Gone too long without sleep, I think. (*Fake excuse*)

Apologies for polluting the interweb, everyone. And thanks to the panel for answerring my question!

-JP

[Jason Bobe]

On Sun, Jul 21, 2013 at 7:01 PM, jarlemag <jarle...@gmail.com> wrote:

Uhh yeah...I should have 30 points substracted from my IQ score I think. I remember looking at the page a long time ago when there were only a few answers, and checked back now to see the same page...and completely failed to nice the "see more" link. Gone too long without sleep, I think. (*Fake excuse*)

Apologies for polluting the interweb, everyone. And thanks to the panel for answerring my question!

No problem.  In the future when we post responses, we will also send a message to the person who submitted the question.

FYI: We have accumulated a small backlog over the past 2 months and the advisory panel is working on a batch on new responses to be posted soon.  The first 6 months we spent quite a lot of time on administrative details, protocols, automation, etc.  

We will be recruiting more expert volunteers into the service at the next ABSA conference this October in KC.  With more contributors, we will improve TAT and expand domain expertise, etc.

Jason Bobe

[Patrik D'haeseleer]

Thanks, Jason!

I have to admit I didn't see the "More" button on the page for a long time either. You might want to rearrange things such that the most recent answer shows on top, rather than at the bottom.

Patrik

[Jason Bobe]

On Tue, Jul 23, 2013 at 3:00 AM, Patrik D'haeseleer <pat...@gmail.com> wrote:

Thanks, Jason!

I have to admit I didn't see the "More" button on the page for a long time either. You might want to rearrange things such that the most recent answer shows on top, rather than at the bottom.

That is on the development backlog.  Thanks!

Jason Bobe

[Jason Bobe]

Last week I made a presentation to the American Biological Safety Association (ABSA) about DIYbio.org's Ask a Biosafety Expert (ABE) service.  I put my presentation up on slideshare:

http://www.slideshare.net/JasonBobe/ask-a-biosafety-expertabe-10232013

One of the main objectives of attending ABSA was to recruit more volunteer biosafety experts into the service.  We've been piloting the service this year, but a lot of time was spent developing operating processes.  We think we''re ready to ramp up the next iteration of the service and hoped to get 8-12 new volunteers by going to ABSA.  About a dozen experts reached out so far, which is really great.    

Jason Bobe

[Patrik D'haeseleer]

Any more answers in the works? It's been a couple months since we saw the last one...

Patrik

On Thursday, January 17, 2013 8:54:25 AM UTC-8, Jason Bobe wrote:

[Jason Bobe]

On Sun, Feb 9, 2014 at 12:41 AM, Patrik D'haeseleer <pat...@gmail.com> wrote:

Any more answers in the works? It's been a couple months since we saw the last one...

Indeed, more answers are in the works.   Back in October, I gave a presentation at the ABSA national meeting and I'm happy to say that the biosafety advisory membership now includes 14 volunteers (up from 3 experts in the pilot).  January was admin / orientation month and last week was the first full week of everyone working together in this second phase of the service.  Draft answers were written for 2 questions in the first few days.

So, for anyone planning experiments or lab work with biosafety related questions, now is a great time to ask:

http://ask.diybio.org/

Jason Bobe

[Jason Bobe]

On Sunday, February 9, 2014 7:32:44 PM UTC-5, Jason Bobe wrote:

On Sun, Feb 9, 2014 at 12:41 AM, Patrik D'haeseleer <pat...@gmail.com> wrote:

Any more answers in the works? It's been a couple months since we saw the last one...

Indeed, more answers are in the works.   Back in October, I gave a presentation at the ABSA national meeting and I'm happy to say that the biosafety advisory membership now includes 14 volunteers (up from 3 experts in the pilot). 

The Ask a Biosafety Expert service has responded to 6 questions over the past few weeks.  Check them out here:

http://ask.diybio.org/questions/

I'll post each question/response individually, so there can be community discussion. 

We are through much of the backlog of questions, so if you are planning some lab work and you have a biosafety related question, now is a great time to ask:

http://ask.diybio.org/

Jason

For BSL1 work, is a hand sanitizer station near the lab exit sufficient?

February 14, 2014

Are there any US regulations I should be aware of related to handling mammalian cell cultures?

February 18, 2014

How do I make my lab BSL-1 compliant?

March 8, 2014

What does a DIY biologist wear?

March 10, 2014

What requirements should I have to conduct safe and harmless experiments?

March 11, 2014

How can I decontaminate electrical equipment used in a wetlab?

March 25, 2014

 

[David Rozak]

Hi Jason, Nice service.  Have you given any thought to building this into something will the serve the role of an Institutional Biosafety Committee for DIY and iGEM groups? 

Dave

[Cat Ferguson]

Hey there,

If you submit this directly to http://ask.diybio.org/ it'll go straight to our experts!

Thanks,

Cat

On Thu, Aug 21, 2014 at 5:13 PM, Mega [Andreas Stuermer] <masters...@gmail.com> wrote:

Hi! 

I was wondering. When I get my construct synthesized that makes bees resistant to viruses. Either I use crispr or siRNA - all the methods require a reverse complementary sequence to an essential viral protein. 

Now, gene synthesis orders are screened not to contain (human?) pathogens, and it is good that they do screen to prevent abuse. 

However, I don't want to be put on a blacklist and maybe get troubles at the airport when travelling to the USA. I heard of a couple in the media who were not allowed to get onto their plane and travel to the USA. Noone refunded their flight tickets. They were just average guys, retired workers. Now immagine, you might get trouble when you're on a blacklist...  

Do you know more about this? 

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http://catferg.com/ 

carolinetay...@gmail.com

(347) 559-6631

Skype: catferguson2

[Bryan Bishop]

On Thu, Aug 21, 2014 at 4:14 PM, Cat Ferguson <carolinetay...@gmail.com> wrote:

If you submit this directly to http://ask.diybio.org/ it'll go straight to our experts!

Are there any reasons why these people are unwilling to use email?

- Bryan
http://heybryan.org/
1 512 203 0507

[Nathan McCorkle]

On Thu, Aug 21, 2014 at 2:13 PM, Mega [Andreas Stuermer]

<masters...@gmail.com> wrote:
> Hi!
>
> I was wondering. When I get my construct synthesized that makes bees
> resistant to viruses. Either I use crispr or siRNA - all the methods require
> a reverse complementary sequence to an essential viral protein.
>
> Now, gene synthesis orders are screened not to contain (human?) pathogens,
> and it is good that they do screen to prevent abuse.

So it seems you're implying the viral protein for the bees will be of
a human pathogen?

FWIW the synthesis-screening stuff is all govt recommendations, there
are no requirements. Likewise, there are no requirements for reporting
these incidents. The govt 'recommends' some protocols for screening to
be used, and 'recommends' sequences that are flagged to be cancelled
from synthesis.

Anyway, we're probably all on the list anyway. Or most of us.

[Patrik D'haeseleer]

This is really more of a science question than a biosafety question anyway.

Viruses mutate very rapidly. So assuming you are targeting a bee pathogen, it if highly unlikely the same sequence will be a close match for a human pathogen as well.

Easy enough to check - just blast your sequence against NR, and check the host range for any hits with sequence identity above 70% or so. I highly doubt that you'll trip any alarms unless you're pretty close to a human pathogen.

Patrik

[Mega [Andreas Stuermer]]

Yeah, 'Tis what I did. 

Deleted the post here, well could have left it too, it seems. 

Cat Ferguson

http://catferg.com/ 

carolinetaylorferguson@gmail.com

(347) 559-6631

Skype: catferguson2

[Bioflukes]

Any DIYBio safety experts here... Need you for an article on labcritics.com. Do reply or mail me at mahboob at labcritics dot com

[Ilya Vainberg Slutzkin]

Hi,

The service seems to be down. I get "ERR_CONNECTION_TIMED_OUT".

Posted my question in the general forum. I hope someone can help me out.

Thanks,

Ilya.

[Jason Bobe]

Will look into it thanks

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