I am curious what you are actually trying to do… You list is far too general for one thing. Is there a particular project that you are building up to…?

“How would you judge the quality of a DNA sequence produced with a closed protocol? ” – That is exactly the issue I am posing here: how to trust open source biology, given that open source software needs to be judged based on the code itself, and often the code has these obvious “FIXME: this is broken but seems to work for now” problems. I don’t have an answer for this, I am raising the question. There is a false analogy made between open biology and open software: with biology, the DNA is not the software and does not contain comments; the DNA is more like machine code, and having machine code of open source software similarly gains little. Not many experts have the time or knowledge to debug and patch binary machine code. The software used to create the DNA sequences has to also be open, and the protocol has to be open, and the means of replicating the biopart also has to be open (reagents, etc), and so on, and only then can trust begin from having many eyeballs looking at the design & implementation.

The code snippet I posted is from an open source package that has no active maintainer and no active bug tracking system. The majority of open source software has no active maintainers and no bug tracking system. There is no way to annotate the code – it is buyer beware or buyer-fix-the-bugs or “buyer trust the code assuming it is in 100% working order.” This is why commercial products go through end-of-life cycles when they are purposely no longer sold, since a company does not want to spend resources to support maintenance costs. Companies are usually not rewarded for that in investors eyes either (investors reward risk and innovation, not so much support contracts). I could also point to comments in the Linux kernel source code that have the same issue (“FIXME This is broken”) — specifically in the IP stack — and yet that code has very active maintainers and tracking systems.

One big innovation in the open biology realm are the PLoS journals which allow the research publications to be publicly annotated. This should provide more trust from having “many eyeballs” looking and commenting on published research. Openwetware.org has attempted to create open bioprotocols, though a wiki format still needs work as a biology collaboration tool to allow better “bug fixing” of the content. Few biologists currently trust protocols posted on Openwetware.org.

But how would you judge the quality of a DNA sequence produced with a closed protocol? How can you say that a sequence database or a public tool is good or bad if you can’t access to what the community says about that, or if you can’t see how quickly bug reports are closed?

Just a naive question: did you write to the author of the library that you posted to tell him that it forgot to fix his code?
It is not fair if you complain about an open source library that you are using but don’t send feedback to the author. You are using a free library, it saves you a lot of time and work and nobody is charging you, so you are at least expected to point out errors when you find them.

This is a mentality that would be very useful if scientists would adopt it. Let’s say that there is an error in a protein-protein interactions database: an open-source minded biologist would write to the authors to tell them the error and how to fix it, while a closed-source biologist would just look at another alternative database, and the error would remain there so other scientists could fall for it.

p.s.: I know most of the software written by biologists is crap, no matter whether it is released freely or not :-)

I haven’t looked into using the USB port with Java. These boards (UBW and Arduino) use a USB chipset that acts like a serial port on the host PC side, so the communication is the same as a terminal/serial device. That way there’s no need to use USB drivers. There are others who have used similar hardware with USB HID controller (keyboard/joystick) drivers with success. Check sparkfun.com forums for info, or Arduino forums.

The code I posted is from a real open source project, though it does not have community support – which is the majority of open source software: unsupported. Even my own open source code, I don’t really support; I put it out there a decade ago in some cases, and it’s buyer beware or buyer improve, whichever is the apt description. Open source gains from having many eyeballs to find & fix bugs, in a thriving community, and often skimps on the unit testing; or, it’s a design to mimic a commercial interface, so the unit test is only obtains coverage where the commercial interface has been previously reverse-engineered.

I use both, and develop both. Specific products have better commercial or better open source packages. The consumer thankfully has a choice in a growing number of arenas now. The choice is not always driven by cost. I will choose a commercial non-linear video editing software product (even at $1500+) way before an open source alternative – with today’s technology.

Now what happens when there is open source bioengineering to act as an alternative to commercial bioengineering? How will you choose? In open source software, it’s possible to look at the code and choose based on design quality and test metrics (for example: compare Linux IP Stack to BSD IP Stack to Microsoft Winsock; Linux is the loser, BSD the winner with even commercial systems adopt BSD, leaving Winsock to be the required evil and avoided if at all possible). In bioengineering, is it possible to look at the code of the design? That remains to be seen, right? The NA sequence is not the code and doesn’t contain comments- it is only the binary operation. The protocols for generating the NA are often closed (unpublished or esoteric), even with open source designs. How is that going to shake out? Especially with so many drawing parallels of open source software to open source biology, often with flawed analogies, it’s an interesting question to consider. At least software can only eat my data. Biology might eat me.

The whole point in this post is misleading because it seems you are saying that closed source code doesn’t have comments like this, and that closed code programmers don’t use ‘FIXME’ or ‘TODO’ comments :-(

The difference between open and closed source is that if you find an error or a wrong behaviour you are able to say that, and the programmers will at least answer you and fix it without charging you for a new version. If you expose an error in the program in a public mailing list, all the users of the software will be able to read it, and if none of the core is able to fix the problem they will be at least aware of it (which is something you can’t have with proprietary software).

Clue 8: Only even numbered transparencies are allowed.

Clue 9: Reading is on a diagonal.

Preparation and Preferences of Peanut-Tempeh, Peanuts Fermented with Rhizopus oligosporus
Masako MATSUO1)
1) Faculty of Home Science, Gifu Women’s University
(Received: October 8, 2005)
(Accepted: September 6, 2006)
In the present study, to develop a new, soft and nutritious peanut product (P-tempeh) to encourage their consumption, peanuts were steamed and were fermented with Rhizopus oligosporus. P-tempeh was suggested to have more free fatty acids than ordinary peanuts and to be readily digestible. Frying and roasting proved to be the preferred ways to prepare P-tempeh. Fried, roasted or steamed, P-tempeh was rated as being more flavorful than soybean-tempeh (S-tempeh), but had 1.7 times the calorific content of soybean tempeh. However, when P-tempeh was prepared with peanuts substituted with 20% quinoa (P8Q2-tempeh), the calorific content decreased to 1.2 times that of S-tempeh. While this made it less preferable in comparison to P-tempeh, it remained comparable with S-tempeh. When P8Q2-tempeh was pre-seasoned with miso, taste scores improved and were similar to those of P-tempeh. Based on these results, when prepared properly, P8Q2-tempeh tastes good, and is a very nutritious and digestible new food source that holds considerable promise.
Keywords: Peanut, Tempeh, Quinoa, Peanut-tempeh

Clue 7: The multiple of row and column designations for each cell is divided by the color number in the spectrum ROYGBIV. Only in these sites can letters be encoded.

More digging into the data:

well#01 index 00 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#02 index 01 rgb= 57,172, 56 hsv=119.48,0.67,0.67 hsl=119.48,0.51,0.45
well#03 index 02 rgb= 64,172, 63 hsv=119.45,0.63,0.67 hsl=119.45,0.46,0.46
well#04 index 03 rgb= 54,172, 53 hsv=119.50,0.69,0.67 hsl=119.50,0.53,0.44
well#05 index 04 rgb= 81,171, 80 hsv=119.34,0.53,0.67 hsl=119.34,0.36,0.49
well#06 index 05 rgb= 96,170, 96 hsv=120.00,0.44,0.67 hsl=120.00,0.30,0.52
well#07 index 06 rgb=132,167,132 hsv=120.00,0.21,0.65 hsl=120.00,0.17,0.59
well#08 index 07 rgb= 60,172, 59 hsv=119.47,0.66,0.67 hsl=119.47,0.49,0.45
well#09 index 08 rgb=159,166,159 hsv=120.00,0.04,0.65 hsl=120.00,0.04,0.64
well#10 index 09 rgb= 71,171, 70 hsv=119.41,0.59,0.67 hsl=119.41,0.42,0.47
well#11 index 10 rgb= 64,172, 63 hsv=119.45,0.63,0.67 hsl=119.45,0.46,0.46
well#12 index 11 rgb= 51,173, 50 hsv=119.51,0.71,0.68 hsl=119.51,0.55,0.44
well#13 index 12 rgb= 24,174, 23 hsv=119.60,0.87,0.68 hsl=119.60,0.77,0.39
well#14 index 13 rgb=156,166,156 hsv=120.00,0.06,0.65 hsl=120.00,0.05,0.63
well#15 index 14 rgb= 93,170, 93 hsv=120.00,0.45,0.67 hsl=120.00,0.31,0.52
well#16 index 15 rgb=139,167,139 hsv=120.00,0.17,0.65 hsl=120.00,0.14,0.60
well#17 index 16 rgb=143,167,143 hsv=120.00,0.14,0.65 hsl=120.00,0.12,0.61
well#18 index 17 rgb= 64,172, 63 hsv=119.45,0.63,0.67 hsl=119.45,0.46,0.46
well#19 index 18 rgb= 67,172, 66 hsv=119.43,0.62,0.67 hsl=119.43,0.45,0.47
well#20 index 19 rgb=143,167,143 hsv=120.00,0.14,0.65 hsl=120.00,0.12,0.61
well#21 index 20 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#22 index 21 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#23 index 22 rgb= 64,172, 63 hsv=119.45,0.63,0.67 hsl=119.45,0.46,0.46
well#24 index 23 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#25 index 24 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#26 index 25 rgb=152,166,152 hsv=120.00,0.08,0.65 hsl=120.00,0.07,0.62
well#27 index 26 rgb= 93,170, 93 hsv=120.00,0.45,0.67 hsl=120.00,0.31,0.52
well#28 index 27 rgb= 24,174, 23 hsv=119.60,0.87,0.68 hsl=119.60,0.77,0.39
well#29 index 28 rgb= 74,171, 73 hsv=119.39,0.57,0.67 hsl=119.39,0.40,0.48
well#30 index 29 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#31 index 30 rgb= 14,175, 13 hsv=119.63,0.93,0.69 hsl=119.63,0.86,0.37
well#32 index 31 rgb= 47,172, 46 hsv=119.52,0.73,0.67 hsl=119.52,0.58,0.43
well#33 index 32 rgb= 14,175, 13 hsv=119.63,0.93,0.69 hsl=119.63,0.86,0.37
well#34 index 33 rgb= 93,170, 93 hsv=120.00,0.45,0.67 hsl=120.00,0.31,0.52
well#35 index 34 rgb= 93,170, 93 hsv=120.00,0.45,0.67 hsl=120.00,0.31,0.52
well#36 index 35 rgb= 34,174, 33 hsv=119.57,0.81,0.68 hsl=119.57,0.68,0.41
well#37 index 36 rgb=146,167,146 hsv=120.00,0.13,0.65 hsl=120.00,0.11,0.61
well#38 index 37 rgb= 14,175, 13 hsv=119.63,0.93,0.69 hsl=119.63,0.86,0.37
well#39 index 38 rgb= 24,174, 23 hsv=119.60,0.87,0.68 hsl=119.60,0.77,0.39
well#40 index 39 rgb=132,167,132 hsv=120.00,0.21,0.65 hsl=120.00,0.17,0.59
well#41 index 40 rgb=162,165,162 hsv=120.00,0.02,0.65 hsl=120.00,0.02,0.64
well#42 index 41 rgb= 96,170, 96 hsv=120.00,0.44,0.67 hsl=120.00,0.30,0.52
well#43 index 42 rgb=113,169,113 hsv=120.00,0.33,0.66 hsl=120.00,0.25,0.55
well#44 index 43 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#45 index 44 rgb=143,167,143 hsv=120.00,0.14,0.65 hsl=120.00,0.12,0.61
well#46 index 45 rgb= 8,175, 7 hsv=119.64,0.96,0.69 hsl=119.64,0.92,0.36
well#47 index 46 rgb=106,169,106 hsv=120.00,0.37,0.66 hsl=120.00,0.27,0.54
well#48 index 47 rgb=156,166,156 hsv=120.00,0.06,0.65 hsl=120.00,0.05,0.63
well#49 index 48 rgb=126,168,126 hsv=120.00,0.25,0.66 hsl=120.00,0.19,0.58
well#50 index 49 rgb=116,168,116 hsv=120.00,0.31,0.66 hsl=120.00,0.23,0.56
well#51 index 50 rgb=103,169,103 hsv=120.00,0.39,0.66 hsl=120.00,0.28,0.53
well#52 index 51 rgb= 14,175, 13 hsv=119.63,0.93,0.69 hsl=119.63,0.86,0.37
well#53 index 52 rgb=146,167,146 hsv=120.00,0.13,0.65 hsl=120.00,0.11,0.61
well#54 index 53 rgb= 30,173, 29 hsv=119.58,0.83,0.68 hsl=119.58,0.71,0.40
well#55 index 54 rgb=106,169,106 hsv=120.00,0.37,0.66 hsl=120.00,0.27,0.54
well#56 index 55 rgb=152,166,152 hsv=120.00,0.08,0.65 hsl=120.00,0.07,0.62
well#57 index 56 rgb= 89,170, 89 hsv=120.00,0.48,0.67 hsl=120.00,0.32,0.51
well#58 index 57 rgb=146,167,146 hsv=120.00,0.13,0.65 hsl=120.00,0.11,0.61
well#59 index 58 rgb= 11,175, 10 hsv=119.64,0.94,0.69 hsl=119.64,0.89,0.36
well#60 index 59 rgb= 86,170, 86 hsv=120.00,0.49,0.67 hsl=120.00,0.33,0.50
well#61 index 60 rgb= 17,174, 16 hsv=119.62,0.91,0.68 hsl=119.62,0.83,0.37
well#62 index 61 rgb=119,168,119 hsv=120.00,0.29,0.66 hsl=120.00,0.22,0.56
well#63 index 62 rgb= 24,174, 23 hsv=119.60,0.87,0.68 hsl=119.60,0.77,0.39
well#64 index 63 rgb= 77,171, 76 hsv=119.37,0.56,0.67 hsl=119.37,0.38,0.48
well#65 index 64 rgb= 38,174, 37 hsv=119.56,0.79,0.68 hsl=119.56,0.65,0.41
well#66 index 65 rgb= 38,174, 37 hsv=119.56,0.79,0.68 hsl=119.56,0.65,0.41
well#67 index 66 rgb= 4,175, 3 hsv=119.65,0.98,0.69 hsl=119.65,0.97,0.35
well#68 index 67 rgb= 24,174, 23 hsv=119.60,0.87,0.68 hsl=119.60,0.77,0.39
well#69 index 68 rgb=126,168,126 hsv=120.00,0.25,0.66 hsl=120.00,0.19,0.58
well#70 index 69 rgb=149,166,149 hsv=120.00,0.10,0.65 hsl=120.00,0.09,0.62
well#71 index 70 rgb= 27,174, 26 hsv=119.59,0.85,0.68 hsl=119.59,0.74,0.39
well#72 index 71 rgb= 96,170, 96 hsv=120.00,0.44,0.67 hsl=120.00,0.30,0.52
well#73 index 72 rgb= 17,174, 16 hsv=119.62,0.91,0.68 hsl=119.62,0.83,0.37
well#74 index 73 rgb= 4,175, 3 hsv=119.65,0.98,0.69 hsl=119.65,0.97,0.35
well#75 index 74 rgb=162,165,162 hsv=120.00,0.02,0.65 hsl=120.00,0.02,0.64
well#76 index 75 rgb= 27,174, 26 hsv=119.59,0.85,0.68 hsl=119.59,0.74,0.39
well#77 index 76 rgb=123,169,123 hsv=120.00,0.27,0.66 hsl=120.00,0.21,0.57
well#78 index 77 rgb= 21,175, 20 hsv=119.61,0.89,0.69 hsl=119.61,0.79,0.38
well#79 index 78 rgb= 51,173, 50 hsv=119.51,0.71,0.68 hsl=119.51,0.55,0.44
well#80 index 79 rgb= 99,169, 99 hsv=120.00,0.41,0.66 hsl=120.00,0.29,0.53
well#81 index 80 rgb= 24,174, 23 hsv=119.60,0.87,0.68 hsl=119.60,0.77,0.39
well#82 index 81 rgb= 93,170, 93 hsv=120.00,0.45,0.67 hsl=120.00,0.31,0.52
well#83 index 82 rgb=136,167,136 hsv=120.00,0.19,0.65 hsl=120.00,0.15,0.59
well#84 index 83 rgb=149,166,149 hsv=120.00,0.10,0.65 hsl=120.00,0.09,0.62
well#85 index 84 rgb=119,168,119 hsv=120.00,0.29,0.66 hsl=120.00,0.22,0.56
well#86 index 85 rgb= 27,174, 26 hsv=119.59,0.85,0.68 hsl=119.59,0.74,0.39
well#87 index 86 rgb= 51,173, 50 hsv=119.51,0.71,0.68 hsl=119.51,0.55,0.44
well#88 index 87 rgb= 38,174, 37 hsv=119.56,0.79,0.68 hsl=119.56,0.65,0.41
well#89 index 88 rgb= 51,173, 50 hsv=119.51,0.71,0.68 hsl=119.51,0.55,0.44
well#90 index 89 rgb=103,169,103 hsv=120.00,0.39,0.66 hsl=120.00,0.28,0.53
well#91 index 90 rgb= 14,175, 13 hsv=119.63,0.93,0.69 hsl=119.63,0.86,0.37
well#92 index 91 rgb= 83,171, 83 hsv=120.00,0.51,0.67 hsl=120.00,0.35,0.50
well#93 index 92 rgb=116,168,116 hsv=120.00,0.31,0.66 hsl=120.00,0.23,0.56
well#94 index 93 rgb= 38,174, 37 hsv=119.56,0.79,0.68 hsl=119.56,0.65,0.41
well#95 index 94 rgb= 57,172, 56 hsv=119.48,0.67,0.67 hsl=119.48,0.51,0.45
well#96 index 95 rgb= 41,173, 40 hsv=119.55,0.77,0.68 hsl=119.55,0.62,0.42

If there’s a problem and you *only* have the sourcecode, there are incredible resources available to the would-be-debugger that computer programmers might only dream about; you can blast your sequence to find similar or identical sequences in the vast DNA databases covering hundreds of species. You can align your gene with similar ones to see the differences. You can use freely available tools to optimise your sequence. You can cut and paste in different regulatory sequences to control it differently.

And finally, if it’s supposed to be advantageous in nature to the organism you’re making it for, you can expect natural selection to debug most of the little issues for you.

Besides, sequencing and synthesis are getting so cheap now that pretty soon you’ll be able to debug and recompile any DNA you want on the cheap. The free availability of the “source code”, though generally expected, won’t even be strictly necessary.

1mm x 1mm pads with 0.5mm gap (or smaller). Though, tried a bunch of different combinations there. The pad size is related to droplet size ( 1 uL of water being well suited to 1.5mm pad size or so). Gap width should be minimized as much as possible without causing shorts or sparks. Sparking can be a big problem.

Cathal – the question is how a user or developer of Open Biology “stuff” can dig down into the “bio source code” when the device fails, or to make an improvement. Interrogating biology is hard enough, and seeing a comment like “/* FIXME – This code is a workaround and might break in the future */” in a re-usable bio part is (currently) impossible. Synthetic parts can use genetic markers, though if I understand, these can go missing over time (as if the comments in code slowly disappear while the program runs). Kind of a far-futuristic-and-currently-moot point of course, since such reusable parts themselves don’t really exist yet.

It is possible to re-broadcast to a different server; it looks something like this:

webcam(s) --USB/VLC--> local PC --VLC--> fast network server <--VLC--> remote viewers using VLC

The local PC sends high-res data. The fast server has different options for limiting the bandwidth, which could include transcoding for lower frame rate, smaller image size, etc. I think my example isn’t really correct for limiting the bandwidth from the video codec: it is supposed to be around 16 kB/sec and it seems higher. It is also possible to have the server embed the video as Flash or WMV in a web page, it only takes a bit of web programming.

As for broadcasting to some video broadcasting service provider, in real-time, I’m not sure. Although frame grabs could be put up on any web host (flickr etc), and video captures could be uploaded to any video service if encoded properly (blip.tv etc). For my bio project, I am most concerned with frame rate and delay, because the robot arms are moving around and I need to see them in actual time. In other bio projects, frame rate probably doesn’t matter, and resolution is more important, so frame grabs might be the best bet there.

My solution is really meant for viewing by 1 remote person, possibly 2 (those running the experiment).

On the microscope+webcam front: I found proof-of-concept good results by literally scotch-taping a Sony PS3 Eye onto the neck of a $50 eBay 40-400X microscope, but I agree that some intermediary optics would be ideal.

Bad software is universal, and I’ve seen far more terrible commercial solutions (usually in niche markets where alternatives don’t exist to drive competition) than open-source ones. Not to mention, an increasing number of commercial solutions are driven at their core by a bunch of open-source libraries and bundles.

Such as, the MacOS I’m using, or the browser I’m typing on, or (chances are) even the software on your server backend, or the database software used to drive this blog.

Don’t *depend* on unproven open-source. But it’s perfectly trustworthy; you can interrogate it when it fails, and find out why. That’s a pretty sound definition of “trust”.

Tito

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design. PerlPrimer is written in Perl and Perl/Tk.

PerlPrimer’s current features include the following:

* Calculation of possible primer-dimers
* Retrieval of genomic or cdna sequences from Ensembl (including both sequences automatically for QPCR)
* Ability to BLAST search primers using the NCBI server or a local server
* Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.
* ORF and CpG island detection algorithms
* Ability to add cloning sequences to primers, automatically adjusted to be in-frame
* QPCR primer design without manual intron-exon boundary entry

One particular project:

Paper: A Perl toolkit for LIMS development. Source Code for Biology and Medicine 2008, 3:4 doi:10.1186/1751-0473-3-4 http://www.scfbm.org/content/3/1/4

ArrayPipeline http://sourceforge.net/projects/arraypipeline/
by chris_trl, james_morris81

ArrayPipeLine is a web-based Laboratory Information Management system, using MySQL, Perl CGI and R. It enables high-throughput analysis of microarray data, providing automation of data handling, and rapid creation and implementation of analysis pipelines

@Note is a Biomedical Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. In fact, it aims to provide support to three different usage roles: biologists, text miners and application developers.

The major guidelines of its development were interoperability, extensibility and user-friendly interface. The workbench is meant for both BioTM research and curation. On one hand, it supports regular curation activities, providing an intuitive Graphical User Interface (GUI) interface that does not require any knowledge about workbench or technique implementation. On the other hand, it is also meant for people with programming skills that might wish to extend the workbench capabilities.

@Note is implemented over AIBench[1], a JAVA framework meant to ease the development of Artificial Intelligence and Data Analysis applications. The main strengths of AIBench are its clear design and available services. Its design is problem-independent, minimum framework-related code is required in order to produce new functionalities. Moreover, it generates GUI code and enforces well-designed MVC code, supporting three main artifacts: operations, data types and views. Operations and data types are used in problem modelling while views display data in a “friendly” way.

Regarding operations, @Note sustains the general workflow of BioTM, fully covering all activities performed in manual curation. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels.

caDNAno is software for design of three-dimensional
DNA origami nanostructures. It was written with the goal of providing a simple and user-friendly interface to facilitate a process that can be complex and error-prone.
caDNAno features:

* No programming required
* Integrated 2D and 3D interfaces
* Visual cues to aid design process
* Export formats: SVG, X3D, JSON
* Platform independent
* Open source (MIT license)

The COnstraint-Based Reconstruction and Analysis Toolbox for Matlab includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models. The Cobra toolbox will work with version 2.0 of the SBML toolbox.

COBRA Toolbox v1.3.3 features

* Reading and writing models in SBML format
*

Reading models exported from the SimPheny program from Genomatica
* Changing model content and parameters: reactions, bounds, objectives, gene associations
*

Network and flux distribution output to Cytoscape
* Common interfaces to a number of free and commercial linear programming solvers
* Flux balance analysis, linear MOMA, and standard quadratic MOMA analysis
* Robustness and double robustness analysis
* Single and double gene deletion analysis
* Dynamic flux balance analysis (batch culture simulation)
* Flux variability analysis
* Uniform sampling of flux space using artificial centering hit-and run
* Tools for statistical analysis of flux samples
* Finding correlated reaction sets
* Reporter metabolite analysis

description from the website: GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more. It is free software under GPL.

http://gentle.magnusmanske.de/

Thanks, Bruce

Any language can work through the named pipe. The Gem_Pipe.pdf documentation that I have is electronic only (which leaves a lot to be desired) and describes all the commands, which are text strings. So the best language to use is one which can handle strings easily. I wouldn’t touch VBScript with a 10 mile pole, since it’s a Microsoft product and limited to running on only their buggy machines. If it’s the only language you know, I suggest learning python which is basic-like. I would bet even Matlab might work to talk to Tecan, since Matlab can handle strings too, though it would be a bit awkward. I wouldn’t want to use C either, because handling the strings wouldn’t be as easy.

In summary I would check out python. There are a few python-for-biologists books (bioinformatics using python) out there.

Do this; google for: tecanprogramming site:groups.yahoo.com. There is a yahoo group which has VBScript source code examples, which I found after writing my post.

I was initially very skeptical of the GUI performance, but I’ve changed my mind a bit. The GUI makes some very intelligent decisions which make life easier, in most cases, so it is still completely usable on it’s own. Things like: changing the number of pipettes which graphically selects wells, or automatically incrementing pipette wells (row or column) within loops, etc. Believe me, I have used supposedly “GUI scripting” equipment with far worse GUI interfaces; in comparison Tecan is doing well with theirs.

Of course it can’t offer the power of, say, running arbitrary Java programs and sending commands over the network… or, running a server which analyzes protocols from protocol-online.org to translate it automatically into Tecan-instructions.. Big things like that need external applications.

My question is, where do I start? I can’t find anything in my manuals about starting off with VBScript, nevermind using another language.

It’s nice to see someone who has merged a love of computers/electronics and science…I can’t seem to find much on it.