[DIYbio] Re: Open Source version of VectorNTI

Benchling (https://benchling.com) is free, pure HTML5 app so there's no installation required. You can check out the demo directly here.
We posted about it just a bit earlier on the DIYBio mailing list. It'll support your plasmid editing needs, as well as sangar sequence trace viewing, basic sequence alignment, primer searching, etc.
Best thing is that it's all online, so you can share sequences with friends and colleagues just via links.



On Saturday, September 28, 2013 8:43:46 PM UTC-7, Dunqiang Liao wrote:
VectorFriends, free for academic researchers. It combines various types of cloning simulations, sequence analysis and data management into one application.

http://www.vectorfriends.com 

On Sunday, February 14, 2010 2:18:47 AM UTC+8, Mackenzie Cowell wrote:
APE - a plasmid editor
http://www.biology.utah.edu/jorgensen/wayned/ape/

Clotho - iGEM project partially by APE, but with additional features for engineering biobricks.
EnzymeX from MekenTosj

I personally recommend clotho: http://vimeo.com/2218118

Cheers,
Mac

On Sat, Feb 13, 2010 at 12:43 PM, Marshall Louis Reaves <marshal...@gmail.com> wrote:
So, Invitrogen did this rather sleazy thing where they got everyone
using VectorNTI because it was free for a long time, and now its not
free, even for academic users.

Does anyone know about any reliable freeware for organizing and
analyzing plasmid sequence data?

Thanks!

MLR

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Very Urgent Requirement for Data Analyst for 1 year contract in NY..

Hello,

Hope you are doing great,

 

Please let me know on Dhruv@riderconsultinginc.com   if you have any good resources for the below position mentioned

 

Role :  Data Analyst - Datastage

Duration :  1 year

Position :  Contract

Location :  Buffalo NY

Interview Process : Phone first F2F in Buffalo or Chicago or NYC or Skype

 

Project Overview

Client is in the process of upgrading the current version of its 3rd party Interest Rate Risk modeling software (QRM), adopting firm-wide standardized risk modeling and chart of account standards, and simultaneously changing data source inputs and creating new QRM data feeds as part of a global initiative to conform to new UK regulatory stress testing reporting requirements. 

 

Project Requirements :

·         Listing and shifting of current QRM configuration of version 14 (set up products, charting of accounts) and move to new release version 16 – regression test of results.

·         Implement and Customize firm-wide global standards platform within QRM for the unique requirements of the impacted North America sites.

 

 

Required Skills :

·         3-5 years Datastage (not coding – that will be done by global team) will be using outputs and functionality

·         Platform is SQL based; ability write queries and manipulate data thru excel and access (Pivot tables and filtering)

·         Heavy Analytical skills regarding

·         Looking at outputs, organizing and manipulating, analyzing and putting back into application

·         Comparing two different feeds and figuring out what differences are

·         Comparing interfaces and how information goes into model along with understanding functionality of data integration layer of global platform and how data is coming through; verifying information is coming thru correctly.

 

Personality Traits

·         Outgoing

·         Analytical

·         Work well with team

·         Excellent Communication skills and talk well with others such as developers, business users and higher level management (presentations)

·         Problem solvers

·         Independent worker

·         Aggressive worker to help push other team members to common goal

 

Pluses:

·         QRM – Quantitative Risk Management system

·         Financial Analysis Background

·         Finance background (rather than Accounting background)

·         advanced capital markets (Swaps and options) is a plus…

·         CFA candidates (not level 1 as this means they are just starting to study for the certification) or certification is a plus

 

 

Thanks,
Dhruv Soni

Phone : 980-272-1261
Email :
Dhruv@riderconsultinginc.com
Gtalk :
dhruvsoni.rider@gmail.com

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Urgent Need !!! QA Manager,Location: Houston, TX

PLEASE SEND  RESUME TO: kavita@tamvid.net OR Saroj@tamvid.net  /Direct: 617.778.2980

Hello,

My name is Saroj Nayak from Tamvid Inc. We are looking for QA Manager .Please let us know if you would be interested for the below requirement. Respond to  me with your updated resume.

Position : QA Manager
Location: Houston, TX
Duration: 1 year
 
Need 10+ yrs of exp
 

Client is implementing a third party Demand Response System which basically will establish the communication between the whole chain from end customer to power grid. The project will have six different streams of work
1.         Product definition
2.         Process for DE Business
3.         Process for DE Upstream
4.         System Implementation
5.         Regulator compliance & Infrastructure
6.         End user technology (Portal, automated end customer equipments)

The person will be expected to create a test strategy across the six stream of work, identify testable scenario, identify interactions between the six streams, identify interactions between the different part of the organization, Identify test cases, business users and coordinate the test cycle and test data.



Regards

Saroj Nayak

Technical Recruiter
TAMVID INC.
100 Trade Center, Suite G700, Woburn, MA 01801
176-25 Union Turnpike, Suite 166, Fresh Meadows, NY 11366
Direct:617.778.2980
E-mail: saroj@tamvid.net
Gtalk:nayaksaroj90
Yahoo:saroj.tamvid
Follow my open jobs @ http://www.tamvid.com/jobs  

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70% de DESCONTO no ÚLTIMO DIA DO MÊS!

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Need: Sr Java Developer / Architect with eCommerce Exp for Boston

PLEASE SEND  RESUME TO: kavita@tamvid.net OR Saroj@tamvid.net  /Direct: 617.778.2980

Hello,

My name is Saroj Nayak from Tamvid Inc. We are looking for Senior Java Developer / Architect Please let us know if you would be interested for the below requirement. Respond to  me with your updated resume.

Position : Senior Java Developer / Architect
Location: Boston
Duration: 3 months

 
We have multiple openings for good J2EE Ecomm java Devs and Architects.
 
Main duties and responsibilities:

·         Design and develop new code and/or support operations, maintenance, and enhancements of existing code using best practices and processes
·         Work and coordinate with various teams - Client, QA, IT, and Offshore team
·         Troubleshooting and bug fixing
·         Estimate and plan iterative / agile releases
·         Identify and escalate risk
·         Handle production issues within defined SLA
·         Mentor team members on the best techniques and processes
 
Requirements:
 
General Skills Needed:

·         Deep understanding on Object Oriented design.
·         Knowledge on design patterns and SOA.
·         ECommerce domain knowledge.
·         Experience working in agile or iterative SDLCs
 
Specific Skills Required for the Project:
·         Expert proficiency in Java and JEE
·         Experience with JSON any ORM framework like iBATIS or Hibernate, REST based WEB API.
·         Performance tuning & debugging.
·         Knowledge on build tools like ANT and Maven and preferably experience on continuous integration tools like Jenkins or Bamboo.
·         Familiar with SQL and / or experience with database technologies such as Oracle.
 
Additional "Would like" Skills and Experience:

·         Client Facing Experience
·         User journeys
·         IA Experience
·         Visual Design Experience
·         Experience in Production Support



Regards

Saroj Nayak

Technical Recruiter
TAMVID INC.
100 Trade Center, Suite G700, Woburn, MA 01801
176-25 Union Turnpike, Suite 166, Fresh Meadows, NY 11366
Direct:617.778.2980
E-mail: saroj@tamvid.net
Gtalk:nayaksaroj90
Yahoo:saroj.tamvid
Follow my open jobs @ http://www.tamvid.com/jobs

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Very Urgent Requirement for Unix Admin in CT- Start ASAP...

Hello,

Hope you are doing great,

 

Please let me know on Dhruv@riderconsultinginc.com   if you have any good resources for the below position mentioned

Role : Unix Admin
Location: Stanford, CT

Duration : 3-6 months – but could go longer
Start date : ASAP

 

 ***Local to NY/NJ/CT candidates only – client will be doing 1st round of phone interviews and then will require a F2F interview as final interview***

Sun Solaris is a MUST HAVE

 

Requirements below:

 

·         Strong In Solaris 9, 10, & 11 (On Sparc & X86) – MUST HAVE THIS EXP.

·         Familiar/Relatively Strong In Windows 2003 Thru 2012 (Mostly 2008r2)

·         Experience With Solaris & Vmware Hypervisors

·         Provide Infrastructure Support To Application & Development Team

·         Interface With Hosted Datacenter Provider Managing Solaris & Windows Farms Virtual Server Farms.

·         Interface With Database Administrator For IBM Informix, Mysql, & MS SQL Issues

·         Troubleshooting Server Operating System Problems, Documentation & Recommendation Of Changes/Patches.  Work With Development & Infrastructure Teams To Ensure Recommendations Are Planned And Implemented As Required. 

·         Experience In Large Dataset Transactions Systems A Plus

·         Experience In Supporting Web Technologies Including Apache, GIT, SQL, JMS, Glassfish, Autosys, PGP

 

 

Thanks,
Dhruv Soni

Phone : 980-272-1261
Email :
Dhruv@riderconsultinginc.com
Gtalk :
dhruvsoni.rider@gmail.com

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Need Senior iOS Developer, Location: Needham, MA(Local Only)

PLEASE SEND  RESUME TO: kavita@tamvid.net OR Saroj@tamvid.net  /Direct: 617.778.2980

Hello,


My name is Saroj Nayak from Tamvid Inc. We are looking for Senior iOS Developer. Please let us know if you would be interested for the below requirement. Respond to  me with your updated resume.

Position : Senior iOS Developer
Location: Needham, MA
Duration: 3 months
 
Must  be local

 

We need a Senior iOS developer in Needham.  The role would be a tech lead for the clients  iPhone eCommerce native app and their iPad-based kiosk.


Regards

Saroj Nayak

Technical Recruiter
TAMVID INC.
100 Trade Center, Suite G700, Woburn, MA 01801
176-25 Union Turnpike, Suite 166, Fresh Meadows, NY 11366
Direct:617.778.2980
E-mail: saroj@tamvid.net
Gtalk:nayaksaroj90
Yahoo:saroj.tamvid
Follow my open jobs @ http://www.tamvid.com/jobs

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Re: [DIYbio] about the peachy printer

It seems like a good product for $100 to me. The three times I saw it brought up in #reprap irc there were negative reactions, but one of the guys already funded it. One person suggested the resin was too expensive, toxic, and the system was too low resolution. But another said that MakerJuice was making it, and it was of comparable cost with ABS by weight.


On Sun, Sep 29, 2013 at 3:59 PM, Jeswin <phillyj101@gmail.com> wrote:
What do the experts on 3d printing say about this product:

http://www.indiegogo.com/projects/the-peachy-printer-the-first-100-3d-printer-scanner

I'm still reading how it works and it seems to have good resolution
for $100. It uses the photolithography method. What do you all think?
Is it good to toy around with? They're only expecting to start
shipping around end of summer of 2014.

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[DIYbio] Re: Extract egg cells from "monthly" ? Possible? Ethical?

Yeah, um, no.

An offer to freeze strangers' tampons or whatever for $500 does not constitute a valid scientific claim. 
Some hints from the website:

>Unfortunately we're short of strict scientific details

uh huh.

>I guess the professional jargon would rather call those cells stromal cells as they are not adult stem
>cells in the sense of being in the adult organism throughout the life and retaining some renewing capacity.

Sorry, not the same thing.

What a very odd business model.
Mega, since you have an interest in eggs and stem cells, you may want to familiarize yourself with the procedures that are normally used.

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[DIYbio] about the peachy printer

What do the experts on 3d printing say about this product:

http://www.indiegogo.com/projects/the-peachy-printer-the-first-100-3d-printer-scanner

I'm still reading how it works and it seems to have good resolution
for $100. It uses the photolithography method. What do you all think?
Is it good to toy around with? They're only expecting to start
shipping around end of summer of 2014.

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[DIYbio] Re: Open Source version of VectorNTI

VectorFriends, free for academic researchers. It combines various types of cloning simulations, sequence analysis and data management into one application.

http://www.vectorfriends.com 

On Sunday, February 14, 2010 2:18:47 AM UTC+8, Mackenzie Cowell wrote:
APE - a plasmid editor
http://www.biology.utah.edu/jorgensen/wayned/ape/

Clotho - iGEM project partially by APE, but with additional features for engineering biobricks.
EnzymeX from MekenTosj

I personally recommend clotho: http://vimeo.com/2218118

Cheers,
Mac

On Sat, Feb 13, 2010 at 12:43 PM, Marshall Louis Reaves <marshal...@gmail.com> wrote:
So, Invitrogen did this rather sleazy thing where they got everyone
using VectorNTI because it was free for a long time, and now its not
free, even for academic users.

Does anyone know about any reliable freeware for organizing and
analyzing plasmid sequence data?

Thanks!

MLR

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[DIYbio] Citizen Science wikibook - Virtual Science Hack with us for the next 24hrs @California Academy of Sciences

Hi All,

We're currently working for the next 24hrs on projects to help the Citizen Science community at the California Academy of Sciences in SF and one of our projects is a Citizen Science Wikibook listing as many of the resources, blogs and tools for Citizen Science as we can, if you have the time and interest we'd really appreciate your input in the wiki!


All the best,

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Re: [DIYbio] Re: Science Hack Day - Useful OS project ideas for the entire DIY Bio community? Anything on your wish list?

This are awesome ideas, thanks everyone! We pivoted to something a little easier a Wikibook for Citizen Science... more to come soon :)

On Thursday, September 26, 2013 2:23:41 AM UTC-7, Cathal Garvey (Phone) wrote:
Odd thing I found was that, on a petri dish, cellulose grew in 'grains' or 'tumours' near but not on bacterial colonies. PreCellulose monomers like to assemble on existing fibers so you get a crystallisation effect rather than a direct association with the producing cells.

Also, cellulose was produced well into stationary, around 5 days or more. Definitely calls for humid incubator to prevent dryout, but also makes for poor differentiation: other species have ample time to overgrow and confuse matters.

Acid is the best first-pass selection system, followed by observation of axenic (single species) plates for cellulose grains.

Patrik D'haeseleer <pat...@gmail.com> wrote:
Yep - that one is definitely on my list of things to try as well. It would be great to have a dye with affinity for cellulose, to definitively identify G. xylinus based on its production of bacterial cellulose. I bet you'll get nice red colonies with Congo red. Not exactly non-toxic though...

Patrik

On Thursday, September 26, 2013 1:41:52 AM UTC-7, Cathal Garvey (Phone) wrote:
It's not chromogenic per se, but when I was isolating G.xylinus from kombucha I used agar with suspended Calcium carbonate: it dissolves as acid is produced. Best poured when very visuous to prevent settling.

Patrik D'haeseleer <pat...@gmail.com> wrote:
Hi Ryan,

One of he projects that has been on my backburner for a while is to develop a chromogenic agar medium from edible ingredients - so we can teach some "biosafety level 0" microbiology demos. The end goal would be to be able to distinguish between colonies of safe microbes such as baker's yeast, lactobacillus from yoghurt, and maybe some kombucha isolates, based on color changes on an agar plate.

Promising chromogenic ingredients include plant pigments that change color with pH such as turmeric and cabbage juice (yeast and kumbucha strains will create a lower pH, so you'll get a colored halo around each colony on the plate). But pretty much any brightly colored foods are worth trying: tomato juice, spinach, saffron, you name it. Make an agar plate with each of them, streak with yeast, lactobacillus and kombucha, and check for differentially colored colonies the next day...

I'm signed up to do a 15 minute lightning talk on DIYbio at Science Hack Day at 11:05, and this is one of the three project ideas I'll be talking about (the other two being Heart in a Jar and steam distillation of essential oils). I've actually been meaning to make a little international DIYbio competition out of this: offer a cash prize for whomever in the DIYbio community comes up with the best, fully documented recipe using all food-safe ingredients that can distinguish between at least two or more food-safe microbes...

By the way, here's an example of a commercial chromogenic agar plate, used to distinguish E. coli from other coliform bacteria in contaminated water. E. coli colonies will be purple/blue and coliform colonies will be pink/red:

http://www.micrologylabs.com/gallery/product_2/coliscan_easygel.jpg

Patrik

On Wednesday, September 25, 2013 12:46:31 AM UTC-7, Biotech Ryan wrote:
Dear All,

As some of you may know the Science Hack day at the San Francisco Academy of Sciences is fast approaching this weekend and we were wondering if you had any ideas or suggestions on projects that the entire DIY Bio community might find useful?

A big group of us are looking to do a project that could benefit the entire DIY Bio community, would be fully open source and in which we could realistically build a prototype within a weekend to share with the broader DIY Bio community. Anything on your wish list? :)

All the best,


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Re: [DIYbio] Re: Longecity: a crowdfunding strategy worth watching

On 09/28/2013 02:17 AM, Mega [Andreas Sturm] wrote:
But it seems to be difficult to correct all the mt -genes. There are many mt per cell.    
You can take a look at some of the open access publications on mitochondrial gene therapy to see whether that's actually the case:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829286/

http://www.discoverymedicine.com/Shilpa-Iyer/2013/03/22/novel-therapeutic-approaches-for-leber-s-hereditary-optic-neuropathy/

I think it's probably harder at this point to measure the degree to which the genes are taken up by mitochondria than to deliver the genes in the first place. Researchers are definitely showing that they can add genes to mitochondria in significant numbers, though:

"Nine to 11 weeks after single exposures to MTD–TFAM + mtDNA complex, PD cybrid cells with impaired respiration and reduced mtDNA genes increased their mtDNA gene copy numbers up to 24-fold, mtDNA-derived RNAs up to 35-fold, TFAM and ETC proteins, cell respiration, and mitochondrial movement velocities."

Reason

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[DIYbio] Re: Extract egg cells from "monthly" ? Possible? Ethical?

http://pimm.wordpress.com/2007/11/06/collect-and-fedex-menstrual-stem-cells-with-the-celle-kit-the-next-flow/

Seems I actually was not that wrong. Stem cells from menstrual blood.

But, not using the egg cells...






On Sunday, August 11, 2013 6:09:06 PM UTC+2, Mega [Andreas Sturm] wrote:
Hi everyone,

---- ----- Those with a strong sense of shame should not read on --- -----


I just came of the idea, that a women loses an egg cell around once a month.
Does anyone have a clue whether it is possible to kind of extract the cell and then have a look on it under the microscope?
I heared those cells are pretty big, so you could even see them with youre bare eye.

Given their size, couldn't you just let the red liquid through a filter, then the big egg cell stays above?

And, one second thought, are those cells still alive when out of body? I mean, they survive 5 days travelling to their destination, sitting there few days, and then are expelled. There won't be mechanism to induce apoptosis I think, because it dies anyway when out of body?



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Re: [DIYbio] Re: Longecity: a crowdfunding strategy worth watching

But it seems to be difficult to correct all the mt -genes. There are many mt per cell.

Expressing them in the nucleus in contrary will take the selective pressure from the mitochondria and these genes will also be deleted in the long term.

IIRC mitos have differing tRNA, carrying different amino acids per codon for a few codons. So you gotta change the language, by synthesizing the genes. The age of cheap synthesizing isn't quite here yet... although it's arriving

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Need: PM with Retail exp,Location - Boston.

PLEASE SEND  RESUME TO: kavita@tamvid.net OR Saroj@tamvid.net  /Direct: 617.778.2980

Hello,


My name is Saroj Nayak from Tamvid Inc. We are looking for PM with Retail exp . Please let us know if you would be interested for the below requirement. Respond to  me with your updated resume.

Position : PM with Retail exp

Duration: 6 months
Location: Boston.  
 
LOCALS preferred.

 
·         If the skill set is strong in Retail & Health, expected to travel within the Boston Metro which includes Hartford, CT & RI
·         Strong in Content Management (i.e. Day or Interwoven).
·         If Ecommerce like Hybris or other package, may have to travel as needed



Regards

Saroj Nayak
Technical Recruiter
TAMVID INC.
100 Trade Center, Suite G700, Woburn, MA 01801
176-25 Union Turnpike, Suite 166, Fresh Meadows, NY 11366
Direct:617.778.2980
E-mail: saroj@tamvid.net
Gtalk:nayaksaroj90
Yahoo:saroj.tamvid
Follow my open jobs @ http://www.tamvid.com/jobs  

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Very Urgent Client Requirement : BA with Pega : NJ : Long Term

Hello,

Hope you are doing great,

 

Please let me know on Dhruv@riderconsultinginc.com   if you have any good resources for the below position mentioned

Role : BA with PEGA Experience
Location : Secaucus, NJ
Duration : Long Term


Required Skills:

 

·         Needs a PEGA Lead with (PEGA MUST) Reporting Analysis experience !!!!!

·         Needs a LEAD person someone who will take ownership of requirements and manage Insurance industry experience.

 

Job Description:

 

·         CRM notes - This position is expected to go through July 2014. The manager wants to stick to the max rate for now.

 

Job Requirements:

 

·         Mandatory: 6 years in a BSA lead role leading large complex and time box projects including Global enterprise project.

·         Ability to conduct/lead workshop sessions and elicit business vision and scope directives from key stakeholders

·         Mandatory: Prior experience in top tier consulting firms a plus and on a similar Global project.

·         Mandatory: Minimum three years' experience in underwriting project in an P&C insurance industry.

·         Ability to take a holistic view of the Property and Energy Underwriting process and define a detailed process roadmap.

·         Ability to work independently to perform Detailed Business Process and Data Analysis.

·         Expand on Sub Business processes as identified in Business System concept Document prepared during Discovery phase

·         Data Analysis: executing data queries and performing data research (via MS Access, PL/SQL, or the equivalent)

·         Ability to articulate thoughts clearly in writing and during business & technical discussions & presentations.

·         Hands-on experience with a full systems life cycle methodology from Requirements Analysis to User Acceptance Testing.

·         Mandatory: Property underwriting Insurance business domain experience (any combination of P&C products).

·         Ability to communicate clearly and effectively with the development team, management, business users, other IT systems owners and DA/DBA group.

·         Excellent communication and presentation skills (verbal and written) used in daily interaction with the Business, CTO and Technical team.

·         Be a self-motivating individual and perform independently in a dynamic environment.

·         Be a strong Team player

 

 

 

Thanks,
Dhruv Soni

Phone : 980-272-1261
Email :
Dhruv@riderconsultinginc.com
Gtalk :
dhruvsoni.rider@gmail.com

 

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Re: [DIYbio] Re: [Biohackers] Open source centrifuge!

Harbor Freight (mostly chinese-imported tool store across USA) sells
dremel-like tools for $9 with accessories, not to mention the always
available %20 off coupons on retailmenot.com

On Thu, Sep 26, 2013 at 11:14 AM, Matthew Harbowy <hbergeronx@gmail.com> wrote:
> In most cases, a 2000g, 6000 rpm minifuge is all you need for mini preps and
> pelleting DNA. Galaxy VWR minifuge for this is $422, brand new, from VWR.
> This kit is $260. You can pick up minifuges at used resellers for <$50. A
> basic Dremel tool is about $50. A replacement rotor for the galaxy microfuge
> (hint, hint) is $70.
>
> To Patrik's point: how much is your eyesight worth? Be careful out there.
> When making plastic covers, use highly resistant materials, like
> polycarbonate laminates (e.g. MAKROLON). Metal rotors are probably a better
> idea than plastic ones. IMO, the brand new minifuge is not so expensive and
> has clearly traceable product liability. DIY in this case might be a great
> learning tool, if by "losing an eye" you learn what not to do.
>
> This has been your "Important safety tip there, Egan" of the day.
>
> Matt
>
> On Thursday, September 26, 2013, Patrik D'haeseleer wrote:
>>
>> I would also want to see what happens to that thin acrylic cover when a
>> fully laden tube ejects from the rotor at full speed. High speed centrifuges
>> are explosion-prone devices, and need to be tested as such. Flying shards of
>> acrylic are no fun...
>>
>> The typical recommendation for using the dremelfuge are to hold it inside
>> a metal cooking pot - at least that will give you some serious protection.
>>
>> Patrik
>>
>>
>> On Thu, Sep 26, 2013 at 10:17 AM, Craig Rouskey <craigrouskey@gmail.com>
>> wrote:
>>>
>>> Thanks Jenny! Typically for DNA work centrifuge speeds need to be approx.
>>> 13000rpm/18000xg
>>> —
>>> Craig J. Rouskey
>>> contact@craigrouskey.com
>>> http://www.craigrouskey.com
>>>
>>>
>>> On Thu, Sep 26, 2013 at 1:15 AM, Jenny Ryan <tunabananas@gmail.com>
>>> wrote:
>>>>
>>>> Via @BiologiGaragen: New open source centrifuge
>>>> http://t.co/otDqV44UER http://t.co/54l7f5DNOt
>>>> Shared via TweetCaster
>>>
>>>
>>>
>>> _______________________________________________
>>> Biohackers mailing list
>>> Biohackers@lists.sudoroom.org
>>> http://lists.sudoroom.org/listinfo/biohackers
>>>
>>
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-Nathan

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