[DIYbio] Re: Paper request

Hi Patricia

No, not at all. Thank you very much, a really cool webside! Thank you as well to anyone else who helped. You guys are awesome!

Cheers Luke


On Tuesday, May 30, 2017 at 7:47:51 PM UTC+2, Patricia P wrote:
Hi Luke,

Are you familiar with Sci-hub? http://sci-hub.bz/

They may move a lot but if you search for them you'll find them

Patricia

On Sunday, May 28, 2017 at 2:17:43 AM UTC-7, Luke wrote:
Hi there

Has anyone acess to this article and willing to share?
Would be lovely.


Kind regards

Luke

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[DIYbio] crispr.kitchen Berlin 7 July with biohacker flea market

CRISPR.kitchen Berlin

first German biohacker and maker gathering


Location: Fab Lab Berlin, 7 July 2017

Open Innovation Space, Prenzlauer Allee 242, 10405 Berlin


The crispr.kitchen connects biohackers and makers who develop their own technologies with industry and academics to exchange about the future of citizen made technology in Germany. By discussing latest prototypes and in interactive games, we will explore the potentials of DIYscience in the innovation system and society.


Program

14:00-14:30 Arrival, setup of tables

14:30-14:40 Opening by Rüdiger Trojok (KIT-ITAS)

and Daniel Heltzel (Fablab Berlin)

14:40-15:00 open Genome hacking and laboratories for everyone

by Rüdiger Trojok

15:00-18:00 Biohacker flea market: show and trade your Biohacks,

Organisms, plasmids, prototypes and materials

18:00-20:00 Grilling the future: food, grill and debate about

the future of citizen made science and innovation

20:00-22:00 Super Bestiary: Playing Tableau Vivant and the

Exquisite Corpse game by Karolina Sobecka


To participate in the flea market register with Rüdiger Trojok rt@openbioprojects.net

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[DIYbio] Re: Downloading JoVE videos?

yeah, i  have the same problem, but  i havent solved it.

在 2016年2月7日星期日 UTC+8下午10:43:12,masoud hasany写道:
I want to download from jove.com, but I can't. plz someone help me. It's only downloaded partially (20 seconds of that). after that we have only sounds.

On Tuesday, September 24, 2013 at 10:25:21 AM UTC+3:30, Patrik D'haeseleer wrote:
So now that JoVE (the Journal of Visualized Experiments) is no longer Open Access - does anyone know of a good way to download their videos locally? The JoVE videos are wonderful, especially for DIYbio practitioners who may have no other way of seeing how these things are done in a real lab.

Someone posted a method a couple of years ago to circumvent their security-through-obscurity by sifting through the html source code, but that approach doesn't seem to be working anymore. I wouldn't be surprised if some version of this still holds though:

http://www.jepoirrier.net/blog/2008/08/jove-and-self-archiving/

I'm especially interested in these videos:

http://www.jove.com/video/50059/procedure-for-decellularization-porcine-heart-retrograde-coronary

http://www.jove.com/video/3740/retrograde-perfusion-filling-mouse-coronary-vasculature-as

http://www.jove.com/video/1138/optical-mapping-of-langendorff-perfused-rat-hearts

Yes, I'm planning to make a ghost heart in a jar for Halloween - can you tell?  :-D

Patrik

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Exclusive Opening || BI Developer

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Hope you are doing great!!

Please go through the requirement and let me know if you are having any consultant for this position.

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Re: [DIYbio] Re: Paper request

There's also a neat little plugin called Unpaywall you can add to your web browser.

On Tue, May 30, 2017 at 1:47 PM, Patricia P <yersinia666@gmail.com> wrote:
Hi Luke,

Are you familiar with Sci-hub? http://sci-hub.bz/

They may move a lot but if you search for them you'll find them

Patricia

On Sunday, May 28, 2017 at 2:17:43 AM UTC-7, Luke wrote:
Hi there

Has anyone acess to this article and willing to share?
Would be lovely.


Kind regards

Luke

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[DIYbio] Re: Paper request

Hi Luke,

Are you familiar with Sci-hub? http://sci-hub.bz/

They may move a lot but if you search for them you'll find them

Patricia

On Sunday, May 28, 2017 at 2:17:43 AM UTC-7, Luke wrote:
Hi there

Has anyone acess to this article and willing to share?
Would be lovely.


Kind regards

Luke

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Re: [DIYbio] Re: Biomedical Engineering or Computer Science Engineering

I think lots of international students go to Germany and Austria, who have hardly any study fees at all. But then, if you want a job or change the world, you'll have to go back to the US, the only country where your genetically enhanced plants/bacteria will ever be allowed outside labs. And still it takes a lot of time there to get approval




On Sunday, May 28, 2017 at 8:36:45 PM UTC+2, Ayush Mahajan wrote:
Which country would be affordable to study Bioengineering ?

On Thursday, May 25, 2017 at 2:58:41 PM UTC+5:30, John Griessen wrote:
On 05/25/2017 04:03 AM, Mega [Andreas Stuermer] wrote:
> Tell the voice in your head to shut up, a lot of people that are less intelligent than you have done it already ;)
>

Repeating an offlist email:
On 05/24/2017 12:43 PM, Ayush Mahajan wrote:
 > thanks, I'm thinking to get Biotech as minor and CSE as majors would
 > this help me overcome my fear?

Only you know your fears very well.  Others have their own fears.

Sometimes fear can be F.E.A.R. ==>  False Evidence Appearing Real.

Finding people doing what you are interested in and asking them how they do it
will dispel any groundless fears, or show you that they do some things
that you are not good at yet, or are avoiding, or maybe even involve fears you have.

Biomedical Engineering channels one into working for companies that get
their designs qualified for medical use, which can be laborious and costly,
especially in the US.

Studying biotech, while also getting a degree in CS
will help you find work outside the medical field.  But both are fairly broad,
not guaranteeing any particular kind of work...

Always be thinking of what work is going to be like, and will you like that,
and ask people that are getting experience again and again what that is like.

also think a lot about what the world needs that you can deliver, or you and some
others can deliver...

If you don't enjoy following others orders like me, that means
learning how to run businesses, and how to get some dirt/land/buildings owned or long term leased
to operate on, so you can do your own thing manufacturing-wise.

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Re: [DIYbio] A question about generating plant calluses

People have used DIY gene guns, which doesn't require agrobacterium which is considered a plant pest. And it's really just pressurized gass shooting DNA-coated metal-nanoparticles into plant cells. Although it's unlikely that that disarmed lab strain remains viable in the wild (they lose their advantage of forcing plant cells to feed them) it may be smart to circumvent any regulatory issues. 

Depending on the strain and plasmids you work with, some antibiotics might work. Kanamycin or streptomycin. Tetracyclin is not recommended as they can develop natural resistance very easily, for what I heard. 

In practiuce you have to subculture the regenerated plantlets several times with antibiotics to make reasonably sure all the agrobacterium will be gone.






On Sunday, May 28, 2017 at 2:36:51 AM UTC+2, Jeff Backstrom wrote:


On Fri, May 26, 2017 at 4:33 PM, Patricia P <yersi...@gmail.com> wrote:
 1.  Do calluses need light to grow?

Most do. Not all.
 
Some protocols grow them in the dark, so I am confused.  If so, what lights/cycle do you recommend?

By the time you generate calli, you will have enough to run experiments. Some in the light, some in the dark. Try 12/12 for those in the light.
 
My purpose for for growing calluses (calli?) would be two-fold: somatic embryogenesis, and transformation with Agrobacter in Crassula. 
 2.  Can I use parafilm to seal the callus-growing petri dishes? What about gas exchange? 

To seal the dishes around the edges? Yes. Parafilm is not air-tight. Carbon dioxide and ethylene will diffuse in and out; ditto with water and oxygen. Parafilm tends to embrittle and get useless after a period of time. You may want to try other plastic wrap like Saran Wrap or other plastic films, or medical paper tape.

 3. Would the PPM in the callus media kill Agrobacter?

Never count on PPM being -cidal. You'll have to run tests on media without selective agents to demonstrate the agro is either gone, or hiding so well that you can't easily find it.

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Re: [DIYbio] Re: How much bioinformatics at your DIY lab?

On 05/29/2017 11:55 AM, Sebastian Cocioba wrote:
> Doing whole genome sequencing on a plant. Used nanopore reads and currently assembling plastid genomes and then will use Amazon
> AWS to do the nuclear assembly. Largest computational project Ive done thus far. Bioinformatics has become the cornerstone of my
> research effects in my home lab.

Sounds close to GMO time. Will you be trying DNA that has some errors from reads and assembly, and do you have any redundant
DNA in there to offset errors?

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Re: [DIYbio] Re: How much bioinformatics at your DIY lab?

Doing whole genome sequencing on a plant. Used nanopore reads and currently assembling plastid genomes and then will use Amazon AWS to do the nuclear assembly. Largest computational project Ive done thus far. Bioinformatics has become the cornerstone of my research effects in my home lab. 

On May 25, 2017 3:40 PM, "Tom Randall" <tarandall@gmail.com> wrote:
The most sophisticated is using standard assemble to reference tools within Galaxy for a fungal genome that I had MWG Operon sequence for me on an Illumina HiSeq machine. See about halfway down this page for a brief description.
http://roningenetics.org/Sequencing.html

Tom

On Tuesday, May 23, 2017 at 4:45:46 PM UTC-4, Patrik D'haeseleer wrote:
Hoping for some quick feedback - How much use to people at your community lab make of bioinformatics? What is the most sophisticated piece of computational work you've done so far? 

At Counter Culture Labs, we have someone doing molecular dynamics simulations for protein linker design. And at BioCurious, we mined some Arabidopsis gene expression data to design novel spatiotemporal promoters. That's about the most sophisticated we've done so far. Other than that, it's mostly some Blast, primer design, codon optimization etc - nothing fancy.

I've been asked to be on a National Academy of Sciences panel this Thursday about synbio and DIYbio (together with Drew Endy, and Tom Burkett from BUGSS), and I'm supposed to talk about how computational tools are enhancing ease of use in DIY labs. Figured I'd do a quick poll of the rest of the community...

Thanks!

Patrik

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Re: [DIYbio] Re: Biomedical Engineering or Computer Science Engineering

On 05/28/2017 01:36 PM, Ayush Mahajan wrote:
> Which country would be affordable to study Bioengineering ?
The USA is not very easy to afford anymore. Don't know about others very much.

There seem to be researchers doing things in Singapore. India is bound to be good.
Taiwan might be good. What is school costing in Australia these days?

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Re: [DIYbio] Re: Biomedical Engineering or Computer Science Engineering

Which country would be affordable to study Bioengineering ?

On Thursday, May 25, 2017 at 2:58:41 PM UTC+5:30, John Griessen wrote:
On 05/25/2017 04:03 AM, Mega [Andreas Stuermer] wrote:
> Tell the voice in your head to shut up, a lot of people that are less intelligent than you have done it already ;)
>

Repeating an offlist email:
On 05/24/2017 12:43 PM, Ayush Mahajan wrote:
 > thanks, I'm thinking to get Biotech as minor and CSE as majors would
 > this help me overcome my fear?

Only you know your fears very well.  Others have their own fears.

Sometimes fear can be F.E.A.R. ==>  False Evidence Appearing Real.

Finding people doing what you are interested in and asking them how they do it
will dispel any groundless fears, or show you that they do some things
that you are not good at yet, or are avoiding, or maybe even involve fears you have.

Biomedical Engineering channels one into working for companies that get
their designs qualified for medical use, which can be laborious and costly,
especially in the US.

Studying biotech, while also getting a degree in CS
will help you find work outside the medical field.  But both are fairly broad,
not guaranteeing any particular kind of work...

Always be thinking of what work is going to be like, and will you like that,
and ask people that are getting experience again and again what that is like.

also think a lot about what the world needs that you can deliver, or you and some
others can deliver...

If you don't enjoy following others orders like me, that means
learning how to run businesses, and how to get some dirt/land/buildings owned or long term leased
to operate on, so you can do your own thing manufacturing-wise.

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[DIYbio] Re: Biomedical Engineering or Computer Science Engineering

Which country which would be affordable to study Bioengineering ?

On Thursday, May 25, 2017 at 2:33:01 PM UTC+5:30, Mega [Andreas Stuermer] wrote:
Tell the voice in your head to shut up, a lot of people that are less intelligent than you have done it already ;) 

It may seem scary at the beginning, but there's a system behind it. And once you see the matrix behind the things, everything makes sense and you know what you need to look up when you get there. 
There will be lab exercises, it's not just theory? 

Me personally, I have had occasions where I wouldn't understand something in detail in a lecture, specifically in no-biotech subjects. But then you either do it in the lab - or just google around connected areas and applications and downstream processes and everything makes sense and the theory is stuck in your head. I never liked learning a row of words in the correct order, I would need to see what the purpose of  "Process X" is and how I can use it, to incentivize my brain to store the info





On Wednesday, May 24, 2017 at 12:13:15 AM UTC+2, Ayush Mahajan wrote:
Yes, I already know how to code, reverse engineer and rest of the stuff which a computer engineer can do, the thing is I want to take BioTechnology for my undergrad but I'm scared because I've never been good with the theory part.I'm interested in coding genome, hacking the wetware and everything Biohacker could do but every time I think about Biotech a voice whispers me in my head saying "Would you be able to do it ?" 


On Sunday, May 21, 2017 at 1:32:38 AM UTC+5:30, Ayush Mahajan wrote:
I've to choose a course now but I'm way too confused between BME and CSE? I'm excellent in coding but I'm interested to learn about this field. My only question is how difficult is it going to be for newbie to start studying about BME and is it a good idea? 

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Re: [DIYbio] Re: Biomedical Engineering or Computer Science Engineering

Which country which would be affordable to study Bioengineering ?

On Thursday, May 25, 2017 at 8:29:20 PM UTC+5:30, Nathan McCorkle wrote:
On Tue, May 23, 2017 at 2:37 PM, Ayush Mahajan <blue...@gmail.com> wrote:
> Yes, I already know how to code, reverse engineer and rest of the stuff
> which a computer engineer can do, the thing is I want to take BioTechnology
> for my undergrad but I'm scared because I've never been good with the theory
> part.I'm interested in coding genome, hacking the wetware and everything
> Biohacker could do but every time I think about Biotech a voice whispers me
> in my head saying "Would you be able to do it ?"

Sounds like I had a similar experience with being good at coding when
I chose a school, but wanting more. The cooler stuff. I've not heard
of computer related protests as much as I have about biotech. Light a
candle and shed some light on the darkness.

Biotech /school/ is mostly just fancy cooking, and learning the theory
is too much to remember for the average student. The 'computer'
processes of life are lots controlled chemical reactions. You don't
need to be so smart as a chemistry major, or a chemical engineer...
biotech has less math requirements than they do. Biotech also has less
math requirements than Computer Science.

Humans engineered electronic computers taught in Computer Science. It
has been around (in text/print/books) for a long time.
Biotech is about reverse-engineering innumerable systems we didn't
engineer. It is like CS for the stuff we didn't engineer.

We are reverse engineering ourselves and all the other species. We are
reverse engineering chemistry, and thus physics.

I know a little about Indian school systems, and if that's where
you're heading towards, you won't have much room to explore
side-studies in your school. The academic programs are very structured
and have strict/tight timelines.

I'd recommend studying biotech, simply because the hands-on and theory
is a lot wider ranging in topic than CS will give you. Also, you can
learn CS at pretty much any hackerspace, free online courses, reading
self-teach books, etc... It is more like 'common knowledge' than
biotech and chemistry/physics. For CS you need electricity and some
relatively common and cheap electronics gizmos. Biotech/lab-science
involves a lot of heavy (mass-wise) stuff, has lots of steps that take
a long time and require a special cook and special kitchen. You can
compile code anywhere your laptop has charge... not as easy to say the
same about a really complex Biotech project.

You can do it. There were many underperforming Biotech students who
received better grades than I did. It's all in how you play the game.
You won't be an underperformer. I know because you're already
self-motivated enough to come post on this online forum. Most students
lack self-motivation. Keep your motivation. It is what keeps you going
in the face of being penniless and without a job. It is a strong
driver of innovation.


All the best,
-Nathan

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[DIYbio] Paper request

Hi there

Has anyone acess to this article and willing to share?
Would be lovely.


Kind regards

Luke

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Re: [DIYbio] A question about generating plant calluses



On Fri, May 26, 2017 at 4:33 PM, Patricia P <yersinia666@gmail.com> wrote:
 1.  Do calluses need light to grow?

Most do. Not all.
 
Some protocols grow them in the dark, so I am confused.  If so, what lights/cycle do you recommend?

By the time you generate calli, you will have enough to run experiments. Some in the light, some in the dark. Try 12/12 for those in the light.
 
My purpose for for growing calluses (calli?) would be two-fold: somatic embryogenesis, and transformation with Agrobacter in Crassula. 
 2.  Can I use parafilm to seal the callus-growing petri dishes? What about gas exchange? 

To seal the dishes around the edges? Yes. Parafilm is not air-tight. Carbon dioxide and ethylene will diffuse in and out; ditto with water and oxygen. Parafilm tends to embrittle and get useless after a period of time. You may want to try other plastic wrap like Saran Wrap or other plastic films, or medical paper tape.

 3. Would the PPM in the callus media kill Agrobacter?

Never count on PPM being -cidal. You'll have to run tests on media without selective agents to demonstrate the agro is either gone, or hiding so well that you can't easily find it.

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Re: [DIYbio] Re: Student subject to criminal proceedings when he uploaded anothers thesis to a share site

"Steal"?

Also, is Jail not a ridiculously out of scale punishment for a dubious and nonviolent offence? This is completely indefensible.

On 27 May 2017 01:19:05 GMT+01:00, Josh Melnick <j.r.melnick@gmail.com> wrote:
Well I wonder what it feels like to have someone steal years of your life, it took many years of hard work for me to write my thesis and wouldn't want others to simply take my work out of my hands.


On Thursday, May 25, 2017 at 9:12:28 AM UTC-5, Abizar Lakdawalla wrote:

After three years of court proceedings in Colombia, a judge in Bogotá acquitted a graduate student yesterday (May 24) of charges he violated copyright law by sharing another researcher’s masters thesis online for a study group. If he had been found guilty, 29-year-old Diego Gomez could have faced years in prison.

This case must spark a serious debate over the necessity of Open Access,” Carolina Botero, director of an organization called Fundación Karisma, which has been helping Gomez with his legal case, said in a press release sent to The Scientist. “Today we celebrate that justice was made in an absurd case that could have set a bad precedent for access to knowledge in Colombia.”

Gomez was studying biology at the University of Quindio in Armenia in central Colombia several years ago when he uploaded another student’s thesis to Scribd, a digital library and e-book and audiobook subscription service. Unlike in the United States, copyright violations in Colombia are a criminal act, and the thesis author pressed charges.

“When uploading the thesis I never thought I was violating any law,” Gomez told The Scientist in 2014. “This type of literature is not of commercial interest, so I never thought I could do any damage to the author. On the contrary, I thought that I was giving him benefits on sharing his work.”

Colombia’s copyright law was born out of an agreement with the United States, intended to bolster trade. “Diego’s story also serves as a cautionary tale of what can happen when copyright law is broadened through international agreements,” the Electronic Frontier Foundation, an advocacy group for free speech and Internet access, posted on its website today. “But as is often the case when trade agreements are used to expand copyright law, the agreement only exported the U.S.’ extreme criminal penalties; it didn’t export our broad fair use provisions.”


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[DIYbio] Re: Student subject to criminal proceedings when he uploaded anothers thesis to a share site

Well I wonder what it feels like to have someone steal years of your life, it took many years of hard work for me to write my thesis and wouldn't want others to simply take my work out of my hands.


On Thursday, May 25, 2017 at 9:12:28 AM UTC-5, Abizar Lakdawalla wrote:

After three years of court proceedings in Colombia, a judge in Bogotá acquitted a graduate student yesterday (May 24) of charges he violated copyright law by sharing another researcher's masters thesis online for a study group. If he had been found guilty, 29-year-old Diego Gomez could have faced years in prison.

"This case must spark a serious debate over the necessity of Open Access," Carolina Botero, director of an organization called Fundación Karisma, which has been helping Gomez with his legal case, said in a press release sent to The Scientist. "Today we celebrate that justice was made in an absurd case that could have set a bad precedent for access to knowledge in Colombia."

Gomez was studying biology at the University of Quindio in Armenia in central Colombia several years ago when he uploaded another student's thesis to Scribd, a digital library and e-book and audiobook subscription service. Unlike in the United States, copyright violations in Colombia are a criminal act, and the thesis author pressed charges.

"When uploading the thesis I never thought I was violating any law," Gomez told The Scientist in 2014. "This type of literature is not of commercial interest, so I never thought I could do any damage to the author. On the contrary, I thought that I was giving him benefits on sharing his work."

Colombia's copyright law was born out of an agreement with the United States, intended to bolster trade. "Diego's story also serves as a cautionary tale of what can happen when copyright law is broadened through international agreements," the Electronic Frontier Foundation, an advocacy group for free speech and Internet access, posted on its website today. "But as is often the case when trade agreements are used to expand copyright law, the agreement only exported the U.S.' extreme criminal penalties; it didn't export our broad fair use provisions."

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[DIYbio] A question about generating plant calluses

Dear plant DIYers,

I am gearing up towards a plant DIY operation, and I was hoping you could answer a couple of questions that I am having a hard time finding on the internet. 

 1.  Do calluses need light to grow? Some protocols grow them in the dark, so I am confused.  If so, what lights/cycle do you recommend? My purpose for for growing calluses (calli?) would be two-fold: somatic embryogenesis, and transformation with Agrobacter in Crassula. 
 2.  Can I use parafilm to seal the callus-growing petri dishes? What about gas exchange? 
 3. Would the PPM in the callus media kill Agrobacter?

many thanks in advance!

Patricia


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Position : Sr. Java Developer with Splunk experience in VA

Hi,


Please find the below position and respond back to me with your profile to praveen@sritechsolutions.com

 

Position : Sr. Java Developer with Splunk experience

Location : Ashburn, VA

Duration:  6+ Months

 

We are looking for individuals who have the ability to write efficient Java code extracting, transforming and loading (ETL) data into Splunk. You must have experience with extracting or exporting data from third party systems using an API or programmatically, and then transforming or formatting the data before loading or pushing the extracted data into a third party application such as Splunk. Excellent communication skills will be required to be effective in this role.

Job Responsibilities:

  • Write high quality, efficient, extensible, commented and maintainable Java code
  • Complete ETL projects collaboratively and efficiently
  • Comment code and develop documentation to support written code
  • Perform code unit test, assembly test and integration testing.
  • Push code to a production environment


Required Experience:

  • Java J2EE skills – minimum 5+ years project experience
  • 8+ years of experience in software development and with Agile or Waterfall experience
  • 3+ years of core Java development: multithreading, dynamic loading, annotation, aspects, events
  • 2+ years of experience with REST, logging, dependency injection, messaging
  • API/REST experience – for loading data into third party systems
  • Ability to understand data models or database tables in third party systems or applications 
  • Experience with a pushing data into third party systems or applications such as Splunk a bonus
  • Advanced debugging, troubleshooting and diagnostic skills across large, distributed, multi-service environments
  • Java microservices


Thanks and Best Regards,

 

Praveen Kumar

SRI Tech Solutions Inc.

praveen@sritechsolutions.com

(T) 1-813-423-6500 X Ext: 149 (M) 248-462 -7719 (F) 813.423.6520

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