Re: Nanoengineer

On Wed, Nov 24, 2010 at 8:55 PM, Lee Nelson <technologiclee@gmail.com> wrote:
> Is there a place on the wiki for this roadmap? Will we use the old wiki?
>
> I advocate using a short (2-4 week) sprint cycle - like they used to. They
> always seemed to make a lot of progress between sprints.
I'd like to suggest creating a new sprint backlog for this group
(which everyone can comment on) and not put a time limit on it. It
will take everyone a while to set up a development environment, get
oriented with the code and start productive coding work.
Here is a quick, short list of the things I believe should be
considered for the 1st sprint:
1. Wiki pages for setting up a NE1 developer's environment for
Windows, MacOSX and Linux. Currently we have these wiki page, but they
need to be updated:
http://nanoengineer-1.net/mediawiki/index.php?title=NE1_Build_and_Release_System_Overview
2. Epydoc install/config on the server to (re)generate NE1 API docs like these:
http://www.nanoengineer-1.com/snapshots/NE1_Documentation/
3. Updated wiki pages for creating NE1 install packages for Windows,
MacOSX and Linux.
4. Set up Bugzilla for NE1 on server (I'm working on this with Bryan
-- stay tuned).
5. Update (and clean up) the NE1 Wiki with new info (i.e. where to get
the code, setting up a NE1 dev environment, etc.) . I've started this,
but more to be done.
These 5 projects would be a good start for the first sprint.
>
> They used Wind IDE for development.
> http://www.nanoengineer-1.net/mediawiki/index.php?search=IDE&go=Go
We used Wing IDE (www.wingware.com). The Personal Edition is $35 and
worth it. I use the Professional Edition and love it.
>
> Since Netbeans has a python plugin, I think netbeans should be used (it is
> free)
> http://www.google.com/search?q=netbeans
I'll take a look at NetBeans. Can you create a "Getting Started with
NetBeans IDE" wiki page explaining what module(s)/plugin(s) to
download and any relevant configuration info.
>
>
> A linux installer/ package is needed to make NE1 accessible to the linux
> crowd.
> There is a new version of BitRock Install builder available.
> http://bitrock.com/
Agreed.
>
> I see there was some change to the build requirements notes regarding QT,
> PyQt and Sip. This is really the only part that prevents a linux install. I
> see the build for Mac but not linux on this Page
> http://nanoengineer-1.net/mediawiki/index.php?title=PreReq_Builds
Maybe Thomas could add something about building NE1 for Fedora on that page?
>
> There was a DNA origami Feature. That should be returned.
The DNA Origami feature was superseded by "Build DNA" and all
sub-commands. Tom Moore actually designed a new origami structure
using NE1 that was eventually synthesized by Paul Rothemund. It was
painful for Tom since NE1 is so slow with large models. It is
imperative to get the graphics optimization in NE1 working (more on
that later).
>
> The movie feature should make AVIs, preferably without needing POV-Ray and
> Picture2AVI as separate programs
This is a feature request. Add it here:
http://www.nanoengineer-1.net/mediawiki/index.php?title=Feature_requests#Other_renderers
>
>
>
>
> On Wed, Nov 24, 2010 at 6:54 PM, Tom wrote:
>>
>> Hi Guys,
>>
>> It's good to see some interest in NE1 again. Do you have any sort of road
>> map for development yet?
>>
>> Best,
>>
>> Tom
>
>
--
-----------------
Mark Sims

Build an AFM files

Index of /books/papers/AFM

 

Gromacs + Blender

Machine Phase

Here is Tom over at Machine Phase blazing a trail of scientific investigation by using Gromacs and Blender.

http://machine-phase.blogspot.com/2010/09/pillared-graphene.html

Blender

blender.org - Download in progress

This is being used to render nano stuff

 

Python 2.7 for Blender?

Will this work? We shall see.

Get Python 2.6 for Blender

Re: Nanoengineer

Is there a place on the wiki for this roadmap? Will we use the old wiki?

I advocate using a short (2-4 week) sprint cycle - like they used to. They always seemed to make a lot of progress between sprints.

They used Wind IDE for development.
http://www.nanoengineer-1.net/mediawiki/index.php?search=IDE&go=Go

Since Netbeans has a python plugin, I think netbeans should be used (it is free)
http://www.google.com/search?q=netbeans


A linux installer/ package is needed to make NE1 accessible to the linux crowd.
There is a new version of BitRock Install builder available.
http://bitrock.com/

I see there was some change to the build requirements notes regarding QT, PyQt and Sip. This is really the only part that prevents a linux install. I see the build for Mac but not linux on this Page
http://nanoengineer-1.net/mediawiki/index.php?title=PreReq_Builds

There was a DNA origami Feature. That should be returned.

The movie feature should make AVIs, preferably without needing POV-Ray and Picture2AVI as separate programs

On Wed, Nov 24, 2010 at 6:54 PM, Tom <mooreth42@gmail.com> wrote:

Hi Guys,

It's good to see some interest in NE1 again. Do you have any sort of road map for development yet?

Best,

Tom

Fwd: IRC channel again

Using Chatzilla,
From the menu, select
IRC -> Join Channel
then enter #hplusroadmap

---------- Forwarded message ----------
From: Bryan Bishop <kanzure@gmail.com>
Date: Wed, Nov 24, 2010 at 6:44 PM
Subject: Re: IRC channel again
To: nanoengineer-dev@googlegroups.com, Bryan Bishop <kanzure@gmail.com>

On Wed, Nov 24, 2010 at 6:39 PM, Lee Nelson wrote:
> Yes, I can participate in the H+ Roadmap IRC channel again. (If I can do it
> from windows for now). Yes I will discuss linux installs of NE-1 with
> people, Yes I will continue to try to package NE-1 for Ubuntu.

Thanks for reviving this old thread. For everyone else, the IRC
channel that he's talking about- and where a lot of ne-1 related
discussion has occured, is:

#hplusroadmap
irc.freenode.net

firefox users: i recommend "chatzilla" and then
irc://irc.freenode.net/#hplusroadmap
everyone else: irssi?

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

Re: Nanoengineer

Hi Guys,

It's good to see some interest in NE1 again. Do you have any sort of road map for development yet?

Best,

Tom

On Wed, Nov 24, 2010 at 7:37 PM, Bryan Bishop <kanzure@gmail.com> wrote:

On Wed, Nov 24, 2010 at 6:27 PM, Lee Nelson wrote:
> Great Bryan. does this mean that you are the official NE-1 maintainer now -

Right. Nanorex has closed their doors. I pinged Mark and asked if I
could help make this happen, so he's letting me run with this.

> or is this a fork? I did not realize that you were active with NE-1.

Heh. Lee, how did you think I spontaneously solved your ne-1 python
problems last year? On the spot, without a reference- over at your
house? Actually I was just winging that.. but yeah, that's how you and
I met I think.

Tom & Thomas:

http://diyhpl.us/cgit/nanoengineer
git clone git://diyhpl.us/nanoengineer

http://groups.google.com/group/nanoengineer-dev

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

DNA Pore

Re: IRC channel again

Yes, I can participate in the H+ Roadmap IRC channel again. (If I can do it from windows for now). Yes I will discuss linux installs of NE-1 with people, Yes I will continue to try to package NE-1 for Ubuntu.

http://www.google.com/search?q=technologiclee+nanoengineer

Thanks for keeping me in mind.

On Tue, Jun 15, 2010 at 3:24 PM, Bryan Bishop <kanzure@gmail.com> wrote:

Hey Lee,

After H+ Summit 2010 and my presentation (it went OK), there have been
some more people in #hplusroadmap - a few of them are interested in
working on Nanoengineer1 and are fairly serious about it. I was
wondering if I could get you back in there so that you can talk about
your experiences with installation nightmares etc.

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

Re: Nanoengineer

On Wed, Nov 24, 2010 at 6:27 PM, Lee Nelson wrote:
> Great Bryan. does this mean that you are the official NE-1 maintainer now -

Right. Nanorex has closed their doors. I pinged Mark and asked if I
could help make this happen, so he's letting me run with this.

> or is this a fork? I did not realize that you were active with NE-1.

Heh. Lee, how did you think I spontaneously solved your ne-1 python
problems last year? On the spot, without a reference- over at your
house? Actually I was just winging that.. but yeah, that's how you and
I met I think.

Tom & Thomas:
http://diyhpl.us/cgit/nanoengineer
git clone git://diyhpl.us/nanoengineer
http://groups.google.com/group/nanoengineer-dev

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

Fwd: Nanoengineer

Bryan, Tom, Thomas


Great Bryan. does this mean that you are the official NE-1 maintainer now - or is this a fork? I did not realize that you were active with NE-1.

Tom was the first person I saw use NE-1.
http://machine-phase.blogspot.com/
Thomas was packaging NE-1 for fedora.
http://web.archiveorange.com/archive/v/OxMZLboVlcHlFDIaa4yo

---------- Forwarded message ----------
From: Bryan Bishop <kanzure@gmail.com>
Date: Wed, Nov 24, 2010 at 6:13 PM
Subject: Nanoengineer
To: Lee Nelson <technologiclee@gmail.com>, Bryan Bishop <kanzure@gmail.com>


Hey Lee,

I have been able to acquire the development repository for ne-1.

http://diyhpl.us/cgit/nanoengineer
git clone git://diyhpl.us/nanoengineer

I'll be maintaining the project from now on. My next step is to
acquire and deploy the original bugzilla database that Nanorex was
using. You should subscribe to the -dev mailing list:

http://groups.google.com/group/nanoengineer-dev

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

Nanoengineer 1 dev group

nanoengineer-dev | Google Groups

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Fwd: [Open Manufacturing] Fwd: [MakerBot] Re: STL files for Atomic Force Microscope

---------- Forwarded message ----------
From: Lee Nelson <technologiclee@gmail.com>
Date: Wed, Nov 24, 2010 at 6:05 PM
Subject: Re: [Open Manufacturing] Fwd: [MakerBot] Re: STL files for Atomic Force Microscope
To: openmanufacturing@googlegroups.com
Cc: diybio <diybio@googlegroups.com>, thingiverse@googlegroups.com


I would like to know the status of the printable AFM.
Has anyone from one of our groups made one?
I searched Thingiverse for "AFM" with no results.
I will try to enter the .stl files into Thingiverse.

On Wed, Jun 16, 2010 at 8:47 AM, Bryan Bishop <kanzure@gmail.com> wrote:

---------- Forwarded message ----------
From: Erik de Bruijn <erikdebruijn1@gmail.com>
Date: Wed, Jun 16, 2010 at 8:42 AM
Subject: [MakerBot] Re: STL files for Atomic Force Microscope
To: MakerBot Operators <makerbot@googlegroups.com>

I sent several requests to the authors of that paper to allow me to
include this on Thingiverse. For one, to attract attention to the fact
that we can push the envelope towards a smaller scale (Plenty of room
there... someone once said!), the second reason is to help further
democratize the toolchain for nano-scale manipulation. Many of these
things can be done with piezzo buzzers and some effort, best practices
should be shared to be able to do this with simple means.

The e-mail I got back from prof. Gaub's colleague:
========
Nice to know that you are interested in our Plastic-AFM design. You
are welcome to include it in your database if you think that it might
be useful for your needs but before some information/premonition.  I
assume that you are aware that the instruction is meant for people
that already have some background in the field of scanning probe
microscopy. Due to limited manpower we cannot give you support on
general AFM issues like handling, calibrating routines, etc. and
furthermore we will not be able to answer specific questions to  your
community members and ask you not to use the gaub@... email address as
reference.

The listed components are only for a lateral movable AFM-head meant
for single-molecule force spectroscopy and no controller-electronics
and software comes along since we use modified commercial products
from the high-end sector for this purpose and assume that users know
how to implement a low-cost alternative (e.g. based on I/O cards and
Labview) that suits their needs. To do AFM imaging one has to combine
it with a x-y-Piezo scanner and the cost per AFM head stays still in
the regime of some thousand Euros.

So if you are still interested feel free to use the design, print/
order the parts and have fun getting a start in the Nano-World.


Regards,
Stefan Stahl
======

I haven't taken the time do put the data on Thingiverse yet, so anyone
feel free to do it.

Erik
http://www.erikdebruijn.nl/

On Jun 15, 5:55 pm, Bryan Bishop <kanz...@gmail.com> wrote:
> On Mon, Jun 14, 2010 at 11:26 AM, Jerry Isdale wrote:
> > Referred to here from Fabaloo article (http://fabbaloo.com/blog/
> > 2010/6/14/do-you-need-an-atomic-force-microscope.html) that notes the
> > full paper costs $ (euros) but the above page gives the basics.
>
> http://designfiles.org/papers/Print%20your%20atomic%20force%20microsc...
>
> Other stuff there might be of general interest:http://designfiles.org/papers/
>
> - Bryanhttp://heybryan.org/
> 1 512 203 0507

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