ABI PRISM 310 Genetic Analyzer working - no software no computer

[Detlef Bohm]

Hello,
I will have an ABI PRISM 310 Genetic Analyzer for 4 weeks from from weekend order to decide to buy or not. This is a good opportunity I had thought for some moments :-(
But I have seen, there is no software (even not the Data Collection Software) availabe for that machine.

At the moment I do not want to contact Applied Biosystems/life technologies whether it can be obtained again.

Any way to get this far old version of software ? 
Any help is very much appreciated

Detlef

[Bryan Bishop]

On Wed, Apr 16, 2014 at 6:57 AM, Detlef Bohm <deti....@googlemail.com> wrote:

But I have seen, there is no software (even not the Data Collection Software) availabe for that machine.

Teardown the machine and let us know the internal equipment- chips, CPUs, connector types, etc. Images will help. Software can be written to probe the capabilities of the machine, and then this will inform us about software to write to make it do things.

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

[Josiah Zayner]

Why not email them?
I have emailed a number of companies and some can be very helpful about obtaining their software or giving control codes to write your own if there is an RS232 port or some such.

[Bryan Bishop]

On Tue, Apr 22, 2014 at 11:02 AM, Josiah Zayner <josiah...@gmail.com> wrote:

I have emailed a number of companies and some can be very helpful about obtaining their software or giving control codes to write your own if there is an RS232 port or some such.

I think they might make money on selling the software, which is often a reason to not send software when asked. But if anyone has a copy, I am interested in taking a look at the files.

[Cory Tobin]

LA Biohackers used to have a 310. We sold it because the laser was
broken and getting a new one would cost just as much as buying a new
sequencer. It also wasn't going to be cost effective in comparison to
outsourcing our sequencing. Anyways...

We managed to get the machine running to some extent. I believe we
found a copy of the software and firmware. You will also need an old
Mac running OS9 with a mac-serial-printer-port.

Regarding the software, we used to have the software on our wiki
(http://wiki.biohackers.la/Gene_Sequencer) but our wiki got destroyed
when we tried to update Mediawiki.

Tor, do you know if we can dump the mediawiki database and pull out
the content for that page? If I remember correctly, there was some
useful info on debugging the sequencer, running the software, etc.
And hopefully the actual file for the 310 software is still sitting on
the server somewhere. I'm trying to browse the mediawiki directory
over SSH but am getting a "permission denied" error.

-cory

[Nathan McCorkle]

can you try browsing using sudo (lets commands run with root
permissions)? Bryan is probably the one to help realistically though!

> --
> -- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
> Learn more at www.diybio.org
> ---
> You received this message because you are subscribed to the Google Groups "DIYbio" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@googlegroups.com.
> To post to this group, send email to diy...@googlegroups.com.
> Visit this group at http://groups.google.com/group/diybio.
> To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAC46JstA6i18TPS6XQhgduCBMiybFajokeBS6ri5%3DjxdtrfzRA%40mail.gmail.com.
> For more options, visit https://groups.google.com/d/optout.



--
-Nathan

[Bryan Bishop]

On Tue, Apr 22, 2014 at 2:32 PM, Cory Tobin <cory....@gmail.com> wrote:

Tor, do you know if we can dump the mediawiki database and pull out
the content for that page?  If I remember correctly, there was some
useful info on debugging the sequencer, running the software, etc.
And hopefully the actual file for the 310 software is still sitting on
the server somewhere.  I'm trying to browse the mediawiki directory
over SSH but am getting a "permission denied" error.

I waste a bunch of time dumping old abandoned mediawiki databases into git repositories. Lately I have been doing this for p2pfoundation's wiki:

http://diyhpl.us/~bryan/irc/p2pfoundation/

I also want to grab transhumani.com, en.bitcoin.it, reprap.org, and a few others eventually. I'd be happy to work on a mediawiki dump from LA Biohackers, but to be clear I won't be interested in deploying mediawiki or fixing your server.

[Detlef Bohm]

Hi all,

I have just seen the answers to my thread (there was a 2-3 days period until it appears, my first post here - Welcome :-)

So far, the machine has not arrived, but my lab is prepared for getting it.

Wow, license and software is a really big part on the cost. I have another offer, getting the machine for € 1500 only, but the software with licence for 3500 :-(
Puh, I do not get the point, why a machine, which had a licence sometime need a new license for such a big amount of money.

@Bryan, if there is a way to get the machine working ? I 'm a programmer (Java) as well. Nevertheless, I'm absolutely lost with these hardware addressing thing.
Unfortunately with this machine you need the software for
1. instrument control
2 data collection.

This - in my eyes - is a big job to solve these issues both.
But, if there is a way in doing that at least partly, I would participate with any information.

Teardown the machine and let us know the internal equipment- chips, CPUs, connector types, etc.

First I will need a computer connected to the machine. Which system ? Windows XP or linux, these are my options.
I will post again, when it will start.

Any recommendations are very welcome !

Cheers
Detlef

[Bryan Bishop]

On Wed, Apr 23, 2014 at 12:49 PM, Detlef Bohm <deti....@googlemail.com> wrote:

@Bryan, if there is a way to get the machine working ? I 'm a programmer (Java) as well. Nevertheless, I'm absolutely lost with these hardware addressing thing.
Unfortunately with this machine you need the software for
1. instrument control
2 data collection.

Sounds like Cory has more direct experience with this machine than I do. My usual process starts with photographs of the parts, then looking at the exact connections, then setting up an environment for recording and replaying signals to the device. Also, knowing the names of the internal microcontrollers is helpful because JTAG can usually grab stuff.

[Cory Tobin]

> Wow, license and software is a really big part on the cost. I have another
> offer, getting the machine for € 1500 only, but the software with licence
> for 3500 :-(
> Puh, I do not get the point, why a machine, which had a licence sometime
> need a new license for such a big amount of money.

OK, so I managed to get a dump of our wiki database and extract some
of our notes using grep - When we talked to ABI years ago about this,
the answer was that the software running on OS9 comes with the
machine. The software running on Windows XP is considered an upgrade
and costs a lot of money. If you go the XP route you'll need a a
converter for serial DB9 (female) to 8-pin mini DIN (male) just to
connect to the sequencer. If you use the OS9 software you'll need a
PPC G3. If you go the OS9 route I may have the CD containing the
software in a cabinet at our lab. I will check this weekend.

Also, for those interested, here is a dump of the firmware from the 310
http://wiki.032.la/gene_sequencer

@Bryan, if you wouldn't mind dumping our database into git, that would
be great. It would be a lot easier finding our ABI310 notes using git
compared to grep :) I could send you the .sql file.

-cory

[Bryan Bishop]

On Wed, Apr 23, 2014 at 3:51 PM, Cory Tobin <cory....@gmail.com> wrote:

@Bryan, if you wouldn't mind dumping our database into git, that would
be great.  It would be a lot easier finding our ABI310 notes using git
compared to grep :)  I could send you the .sql file.

Sure, I'll take that. yoink.