Re: [DIYbio] Gel Red questions

SYBR Safe and Thiazole Orange are very similar, but not identical.  So is Thiazole Orange an acceptable substitute for the more expensive SYBR Safe in gel staining?  If so, why isn't everyone using it?

Thiazole Orange is membrane-permeable.  It was first developed to label RNA in intact reticulocytes.  I'm pretty sure that Thiazole Orange also binds DNA.  All DNA intercalating dyes are suspected carcinogens, for obvious reasons.

One way that SYBR Safe might be "safer" than Thiazole Orange is if the former was membrane-impermeant.  Is it?  I doubt it.  If anything, I would expect SYBR Safe to be slightly more membrane-permeant, because SYBR Safe has a propyl group where Thiazole Orange has a methyl group.  However, that structural change might also reduce toxicity.

I just had a look at an MSDS for each compound, and I didn't see any obvious differences.  



On Thursday, April 27, 2017 at 1:49:25 PM UTC-7, Dennis Oleksyuk wrote:
It is much cheaper here if you buy 5G at a time.

On Wed, Apr 26, 2017 at 5:06 PM Mega [Andreas Stuermer] <masters...@gmail.com> wrote:







On Sunday, April 23, 2017 at 10:03:09 PM UTC+2, John Ladasky wrote:


On Tuesday, March 12, 2013 at 12:03:42 PM UTC-7, Nathan McCorkle wrote:
Yeah, that's why big companies and universities don't switch.

EtBr is molecularly known (no one really knows exactly what the gelRed
and sybrSafe molecules are, we know what classes they're in or one
that was described in one patent, etc)

I'm pretty sure that this information cannot be kept secret.  To obtain a chemistry patent, and to publish an accurate MSDS, the structure of the novel active compound must be known and disclosed.

I remember that SybrSafe is in the cyanine dye family, a descendant of Thiazole Orange.  If you look at the Wikipedia article for SybrSafe, a structure is published, and it sure looks like a cyanine dye to me.

 
Wikipedia entries are also available for GelGreen and GelRed.  They look like acridine orange and ethidium dimers, respectively, with a peptide-ether linker between the individual fluorophores.


The idea of making ethidium dimers is not new.  An ethidium dimer was available in 1990.  It's still available.  The linker differs from the GelRed linker, but otherwise the two molecules are quite similar.



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[DIYbio] Re: Molecular Biologist looking for collaborator for a Metabolic Modelling Project

Hello Ravasz,

Thank you for your reply and sorry for replying to you only now. I only just saw this!

I am glad to hear you are willing to help. Can you write on here an e-mail address I can contact you on?

Cheers,

Paolo

Il giorno sabato 25 marzo 2017 10:40:50 UTC, Ravasz ha scritto:
Hi there,

I'm another molecular biologist / bioinformatician also in Edinburgh. I know little about modelling per se, but I'm teaching python to biologists and I'm an avid DIYbio person, so I am certain we can come up with something if you need help. If you want to meet up just let me know, I'm at King's Buildings.

Cheers,
Mate


On Friday, 24 March 2017 18:35:14 UTC, Paolo Marangio wrote:
I am a Molecular Biology Resarch Assistant based in Edinburgh and I recently came across an interesting paper where they used modelling for coming up with deletion strategies that allow increased production of cis-aconitic acid in E. coli (you can read all about it here: https://www.ncbi.nlm.nih.gov/pubmed/27269589). SInce I found this approach particularly powerful, I decided to do some modelling out of interest. I am planning on using the python package Cobrapy for this (http://opencobra.github.io/cobrapy/) as I don't know how to use MATLAB. After I will have identified some deletion strategies, I could test them directly as I have access to a lab. I was therefore wondering if there is anybody on here who has experience with this package or constraint-based modelling in general and would like to collaborate in this small project. 

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Re: [DIYbio] Molecular Biologist looking for collaborator for a Metabolic Modelling Project

Dear Francis,

Thank you very much for your reply! Sorry for my late reply, I only just saw this!

I am already a member of the cobraby google group. Cool, can you write here an e-mail address I can contact you on?

Cheers,

Paolo

Il giorno venerdì 24 marzo 2017 18:56:00 UTC, Francis Lee ha scritto:
There's a decently active group that's dedicated to cobrapy:


They might have a larger pool of experienced users.

Otherwise I've used cobrapy a few times before, and I'm happy to chat a bit more with what you're interested in doing.

Francis

On Fri, Mar 24, 2017 at 2:30 PM, Paolo Marangio <marang...@gmail.com> wrote:
I am a Molecular Biology Resarch Assistant based in Edinburgh and I recently came across an interesting paper where they used modelling for coming up with deletion strategies that allow increased production of cis-aconitic acid in E. coli (you can read all about it here: https://www.ncbi.nlm.nih.gov/pubmed/27269589). SInce I found this approach particularly powerful, I decided to do some modelling out of interest. I am planning on using the python package Cobrapy for this (http://opencobra.github.io/cobrapy/) as I don't know how to use MATLAB. After I will have identified some deletion strategies, I could test them directly as I have access to a lab. I was therefore wondering if there is anybody on here who has experience with this package or constraint-based modelling in general and would like to collaborate in this small project. 

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[DIYbio] Re: Why are PCR machines and biotech equipment in general so expensive

I just wanted to elaborate on this statement here:

"
In my personal opinion, the only value in developing yet another version of PCR is educational. 
You mean to say only educational institutes would buy? What about existing researchers, diagnostic labs and biohackers. 
"

When I asked around my academic workplace for old, free equipment that we could donate to our local community lab, I immediately got offered 2 functioning PCR machines. I turned them down because the community lab had 5(!) already, and in reality only actually needed one. It turns out for academic institutions, PCR machines are cheap already and new ones are bought every now and then from leftover grant money just to replace the older units in case they ever fail.

A perfectly good, new, branded PCR machine costs $1000-2000. Compare that to the cost of standard lab consumables which are like $100 for a 1 day experiment for 1 researcher, or to the cost of a simple mass spectrometer, DNA sequencer or fluorescence microscope which are easily above $100K each.

Working for years to bring down the cost a new open source PCR machine from $1000 to $800 is great, but it won't really affect academic labs and biotech companies. They will buy the same $2000 branded PCR machine anyway as for them it costs peanuts, and they realize that reliability is everything: if your branded machine is reliable 98% of the time and your open source machine only 95%, they you will easily recover the cost of the branded PCR machine in no time due to the cost saved by having to repeat less experiments.

So the only gain from developing a new PCR machine is really the learning experience you get, so the educational opportunity as said above. You cannot base a business model on it.

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Re: [DIYbio] Why are PCR machines and biotech equipment in general so expensive

Hi Ujjwal,

Well congratulations on persevering on your project over the past year!

I think there is a common mistake some people on this forum make, which is concentrating on the BOM cost. They make this mistake because coming from a DIY background, their vast amounts of personal time are unaccounted for, and the only costs they see are material costs. But that is not how a business runs.

Here's what those people don't see. Consider a popular video game sold over the Internet. It might be sold for $50. The actual cost to transmit the game might be pennies, which is the closest equivalent to BOM costs. The rest of that $50 goes to fixed development costs, transactional costs, marketing, distribution costs (resellers), customer support, and hopefully a small amount of profit.

Hardware is just like the video game, except that in addition to all those costs, the BOM/COGS cost is very significant as well.

Rarely have I heard someone object to the $50 video game price because it only costs pennies to transmit. But once hardware is involved, some people become infatuated with the BOM costs, neglecting all the other costs. This is a big mistake in general, but doubly so in biotech, where the volumes are small compared to a video game, but fixed development costs equally large, so those fixed costs have to be spread across a smaller number of units. This is why biotech equipment in general is so expensive.

OpenPCR was never intended to be a business. It was a personal project between me and a friend, and initially we didn't even intend to sell kits but just release an open source design. Honestly it was started before I understood the above, and being a software person at the time, I also didn't understand the R&D effort required. The project stemmed from a conversation during a long car trip. I think at the time I thought it would be a 2 week project, and it ended up consuming 1.5 years of my life :) I learned a lot, but OpenPCR was never about making money.

Chai is different. We've raised millions from Silicon Valley investors. The concept behind Chai is not to make low cost equipment, but to expand molecular diagnostics to valuable industrial applications. Doing that necessitated making things easier and cheaper. Honestly our devices are priced out of the reach of most biohackerspaces, but we're focussed on continuing to reduce the costs of molecular diagnostics to expand the market size. Eventually this technology will be affordable even to consumers.

-Josh


--
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CEO

Chai
3206 Scott Blvd | Santa Clara, CA 95054
Tel: +1 (650) 488-8550 | Mobile: +1 (650) 469-3222

On Fri, Apr 28, 2017 at 4:55 AM, Ujjwal Thaakar <ujjwalthaakar@gmail.com> wrote:
Hi Josh,
I spent most of the last year learning to make hardware and have a prototype ready. It's not great and market ready yet. Turns out I highly underestimated what it takes to build a product.

Now I'm trying to figure out the business opportunity. What has been your experience at Chai as the original pioneer of low-cost PCR? What has the market response been like and what difficulties have you faced. A lot of people on this forum including me talk about developing open source low-cost equipment but what reality are we missing that you have experienced since you are one of the handfuls to have actually built a successful company out of this.

On Sun, Apr 23, 2017 at 1:47 PM Josh Perfetto <josh@snowrise.com> wrote:
Dennis said it perfectly on all 3 counts.

Ujjwal I thought you were going to develop lower cost PCR. What has stopped your efforts from succeeding?

-Josh


-Josh

On Fri, Apr 21, 2017 at 8:47 AM, Dennis Oleksyuk <dennis@oleksyuk.me> wrote:
Because building hardware is harder than building software. It requires more skills, time, and money. That's the main reason which applies to hardware development as a whole.

Because the number of customers who buy scientific equipment is small. Therefore the manufacturer has to divide the development cost between a smaller number of customers.

Because the cost of consumables and labor for solving a particular problem is usually higher than the cost of the machine. Therefore the buyers are more interested in saving in labor and consumable cost rather than hardware prices.


On Fri, Apr 21, 2017 at 8:42 AM Gerald Trost <gerald.trost@mail.com> wrote:

this is only my honest opinion from my experience:

I bought a open source 3d printer - in industry they had
such things for 3 decades - but they costed
several hundred thousands

the open source thing works fine but for 90% of the time
its in maintenance and I am the machine engineer

I think the open source things are not yet reliable enough.
 
Sent: Friday, April 21, 2017 at 1:57 PM
From: "Ujjwal Thaakar" <ujjwalthaakar@gmail.com>
To: DIYbio <diybio@googlegroups.com>
Subject: [DIYbio] Why are PCR machines and biotech equipment in general so expensive
How do the economics work out and why have we not seen bigger companies bring down the process in the advent of open source equipment as well as new startups building low-cost equipment?

 

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Re: [DIYbio] Why are PCR machines and biotech equipment in general so expensive

In my personal opinion, the only value in developing yet another version of PCR is educational. 
You mean to say only educational institutes would buy? What about existing researchers, diagnostic labs and biohackers. 

Regarding your other suggestion, I actually started because I wanted a machine of my own. I have performed PCR a couple of times.

On Fri, Apr 28, 2017 at 7:37 PM Dennis Oleksyuk <dennis@oleksyuk.me> wrote:
Hi Ujjwal,

To figure out the business opportunity you need to ask real custom about their needs or, even better, become your own customer. I suggest you find a molecular biology lab and go do some experiments there. Order some gene, PCR it into the plasmid, put it into the bacteria, and somehow quantify its effect.

In my personal opinion, the only value in developing yet another version of PCR is educational. 

On Fri, Apr 28, 2017 at 7:56 AM Ujjwal Thaakar <ujjwalthaakar@gmail.com> wrote:
Hi Josh,
I spent most of the last year learning to make hardware and have a prototype ready. It's not great and market ready yet. Turns out I highly underestimated what it takes to build a product.

Now I'm trying to figure out the business opportunity. What has been your experience at Chai as the original pioneer of low-cost PCR? What has the market response been like and what difficulties have you faced. A lot of people on this forum including me talk about developing open source low-cost equipment but what reality are we missing that you have experienced since you are one of the handfuls to have actually built a successful company out of this.

On Sun, Apr 23, 2017 at 1:47 PM Josh Perfetto <josh@snowrise.com> wrote:
Dennis said it perfectly on all 3 counts.

Ujjwal I thought you were going to develop lower cost PCR. What has stopped your efforts from succeeding?

-Josh


-Josh

On Fri, Apr 21, 2017 at 8:47 AM, Dennis Oleksyuk <dennis@oleksyuk.me> wrote:
Because building hardware is harder than building software. It requires more skills, time, and money. That's the main reason which applies to hardware development as a whole.

Because the number of customers who buy scientific equipment is small. Therefore the manufacturer has to divide the development cost between a smaller number of customers.

Because the cost of consumables and labor for solving a particular problem is usually higher than the cost of the machine. Therefore the buyers are more interested in saving in labor and consumable cost rather than hardware prices.


On Fri, Apr 21, 2017 at 8:42 AM Gerald Trost <gerald.trost@mail.com> wrote:

this is only my honest opinion from my experience:

I bought a open source 3d printer - in industry they had
such things for 3 decades - but they costed
several hundred thousands

the open source thing works fine but for 90% of the time
its in maintenance and I am the machine engineer

I think the open source things are not yet reliable enough.
 
Sent: Friday, April 21, 2017 at 1:57 PM
From: "Ujjwal Thaakar" <ujjwalthaakar@gmail.com>
To: DIYbio <diybio@googlegroups.com>
Subject: [DIYbio] Why are PCR machines and biotech equipment in general so expensive
How do the economics work out and why have we not seen bigger companies bring down the process in the advent of open source equipment as well as new startups building low-cost equipment?

 

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Urgent Client Need: Big Data Architect; Boston MA; 6-12 Months Contract ( Locals Only)

Please send your resumes at niranjan.kumar@vision3solutions.com

 

Hi

 

This is Niranjan from Vision3solutions; hope you are doing well.

Please go through below description and reply with your resume, contact details and current location, if you feel comfortable

 

 

Job Title: Big Data Architect

Location: Boston MA

Duration: 6-12 Months Contract


Interview: Telephonic AND Face to Face

 

Department:  Data Analytics R&D

Job Category: Software

                 

Duties:              

The Client Big Data Engineering team is a group of engineers that are passionate about data. We are responsible for the complete data pipeline from processing raw data to applying analysis of the data. Our team is responsible for the designing and development of tools and systems for the entire lifecycle of data; data collection, data processing, monitoring, data quality and correction, data access platforms and more. We are looking for driven people to help us build the next generation platform for TV analytics.

 

Responsibilities:

·         Architect a multi-tier data pipeline to feed data into an OLTP application in addition to an analytics environment

·         Design and build schemas to handle large scale interactive reporting

·         Design and build ETL/ELT process to move data through the data processing pipeline.

·         Manage complex data dependencies across datasets and incremental data loading workflows.

·         Be a fearless leader in championing smart design

·         Love scaling systems

 

Skills:

·         A Bachelor's or Master's degree in computer science or software engineering

·         Hands on experience with Big Data stack of technologies –Hadoop, HDFS, Hive, Hbase

·         Strong expertise in Java Map/Reduce and Python

·         Experience with Amazon web services: On demand computing, S3, and EMR (Elastic Map Reduce) or equivalent cloud computing approaches

·         Hands on experience with Apache Spark using Scala or Python

·         Strong expertise in Data Warehousing and analytic architecture

·         Deep expertise in writing complex SQL and ETL batch processes

·         Experience working with large data volumes

·         The ability to get code in to production

·         A pro-active go get it attitude

·         The desire to automate the first time

 

Nice to Have

·         Columnar and MPP database - Redshift, or similar technologies

·         Shell scripting experience

·         Strong knowledge of and experience with statistics

·         Ability to performance tune the SQL

 

What Skills should you have?

·         Must have firm understanding of database systems – Data modeling, SQL query Processing and Transactions Know how to scale systems and make them fast!

·         Experience debugging and tracing SQL performance issues

·         Solid understanding of software development from design and architecture to production.

·         Large scale DW, MPP, Redshift, or similar technologies

·         Solid math skills.

·         The ability to present impromptu and via a whiteboard

 

Bonus points for:

·         Experience with the Hadoop ecosystem (HBase/Hive/map reduce)

·         Experience working in AWS

·         Knowledge of Tableau

·         Experience with Redshift or ParAccel/Actian Matrix

·         Experience with Pentaho Kettle

·         Linux basics

·         Big, Big bonus if you know a programming language or two.

 

 

Thanks& Regards

 

Niranjan Kumar

 

cid:image001.jpg@01D0705F.83E60BC0

 

Vision3 Solutions Inc

8155 Cavendish Place,Suwanee, GA 30024
Contact No:
(678) 554-4785
Email: niranjan.kumar@vision3solutions.com

                 niruk5503@gmail.com

 

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Urgent Client Need: Big Data Architect; Boston MA; 6-12 Months Contract ( Locals Only)

Please send your resumes at niranjan.kumar@vision3solutions.com

 

Hi

 

This is Niranjan from Vision3solutions; hope you are doing well.

Please go through below description and reply with your resume, contact details and current location, if you feel comfortable

 

 

Job Title: Big Data Architect

Location: Boston MA

Duration: 6-12 Months Contract


Interview: Telephonic AND Face to Face

 

Department:  Data Analytics R&D

Job Category: Software

                 

Duties:              

The Client Big Data Engineering team is a group of engineers that are passionate about data. We are responsible for the complete data pipeline from processing raw data to applying analysis of the data. Our team is responsible for the designing and development of tools and systems for the entire lifecycle of data; data collection, data processing, monitoring, data quality and correction, data access platforms and more. We are looking for driven people to help us build the next generation platform for TV analytics.

 

Responsibilities:

·         Architect a multi-tier data pipeline to feed data into an OLTP application in addition to an analytics environment

·         Design and build schemas to handle large scale interactive reporting

·         Design and build ETL/ELT process to move data through the data processing pipeline.

·         Manage complex data dependencies across datasets and incremental data loading workflows.

·         Be a fearless leader in championing smart design

·         Love scaling systems

 

Skills:

·         A Bachelor's or Master's degree in computer science or software engineering

·         Hands on experience with Big Data stack of technologies –Hadoop, HDFS, Hive, Hbase

·         Strong expertise in Java Map/Reduce and Python

·         Experience with Amazon web services: On demand computing, S3, and EMR (Elastic Map Reduce) or equivalent cloud computing approaches

·         Hands on experience with Apache Spark using Scala or Python

·         Strong expertise in Data Warehousing and analytic architecture

·         Deep expertise in writing complex SQL and ETL batch processes

·         Experience working with large data volumes

·         The ability to get code in to production

·         A pro-active go get it attitude

·         The desire to automate the first time

 

Nice to Have

·         Columnar and MPP database - Redshift, or similar technologies

·         Shell scripting experience

·         Strong knowledge of and experience with statistics

·         Ability to performance tune the SQL

 

What Skills should you have?

·         Must have firm understanding of database systems – Data modeling, SQL query Processing and Transactions Know how to scale systems and make them fast!

·         Experience debugging and tracing SQL performance issues

·         Solid understanding of software development from design and architecture to production.

·         Large scale DW, MPP, Redshift, or similar technologies

·         Solid math skills.

·         The ability to present impromptu and via a whiteboard

 

Bonus points for:

·         Experience with the Hadoop ecosystem (HBase/Hive/map reduce)

·         Experience working in AWS

·         Knowledge of Tableau

·         Experience with Redshift or ParAccel/Actian Matrix

·         Experience with Pentaho Kettle

·         Linux basics

·         Big, Big bonus if you know a programming language or two.

 

 

Thanks& Regards

 

Niranjan Kumar

 

cid:image001.jpg@01D0705F.83E60BC0

 

Vision3 Solutions Inc

8155 Cavendish Place,Suwanee, GA 30024
Contact No:
(678) 554-4785
Email: niranjan.kumar@vision3solutions.com

                 niruk5503@gmail.com

 

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