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Fair enough. Do, please, find me Open Source alternatives for the following software packages, so I can tell the laboratory I work for, to dump all Windows-only software, that has been certified that the results will hold up legally in court, and run this new stuff that you have found:
https://products.appliedbiosys...

ChemoView by AB Sciex
NI Curl
NI Dynamic Acquisition
NI MetaSuite
WinTox
SmartCycler/LightCycler

Most of these software packages run on multi-million dollar laboratory instruments, FYI. Some of them, *mandated* by the Federal gov't, ONLY run under WinXP SP1 (how's that for a gotcha?)

As far as Linux goes, I stand corrected, someone else pointed out he must be a raving Linux fan as only they can be so blind as to think Linux solves all issues.

So, do find me alternatives, and that's just for starters. Much of what we run is very specialized and.simply.doesn't.exist outside of the Windows environment.

Step into the real world of business one day, you'll see what works, and what doesn't.
(BTW, I'm working, in my own time, on RNNs through Ubuntu 16.04 LTS and CUDA supported nVidia cards. I am a Linux fan)

It shows the sad state of public knowledge of genomics that this was modded informative.

Techniques are currently available to isolate single bacterial cells from environmental samples and sequence the fragments of their genomes. The sequencing is likely done with one of these, or something similar:

https://products.appliedbiosystems.com/ab/en/US/ad irect/ab?cmd=catNavigate2&catID=600533

which is old technology now, but I'm not going to bother mentioning the new kinds of machines.

The company plans to leverage its patented technology in accelerated thermal cycling through licensing and internally developing devices for clinical diagnostics, general biotechnology, bio-defense and other related industries.

Yay for another patent on PCR technology, only a few months after the original PCR patent has expired. But of course they're only going with the trend -- there's other patents on PCR and associated technologies.

ctually, the irony of your statement is that we're going to need better nano-technology to complete the task.

No. Nanotechnology is completely uninvolved in this. These guys are chemists, biochemists & geneticists not engineers.

As enthusiastic as these companies are, the problems in intentionally constructing a DNA molecule letter by letter are huge: notably, if you screw up in one spot, you can have tremendous problems.

No. Making DNA base by base is not difficult at all, and has not been for many years. DNA synthesizers can churn out oligos of good purity of lengths into the 100s of bases. Need longer? Make ligatable overhangs and have an enzyme put them together, ligation techniques are trivial molecular biology. As for mistakes, of course they happen, but any scientist worth her salt would sequence it along the way. Remember that Human genome project thing? That was just a lot of DNA sequencing. The machine mentioned in the long article as a long seqeunce synthesizer is just a robotic version of a bench biochemist doing what i described.

Further, there's no "spell check" for them, using current methods. They wouldn't know they had a problem until they start letting it reproduce, only to find that they have an [apparently] inexplicably error, possibly making the organism unviable.

No spell check of making sequences? True, sort of. During the synthesis there isn't, but sequencing it post symthesis is absolutely trivial.

Whats needed is sophisticated enough nanobots that will be able to not only perform the construction of the DNA, but to "spell check" it by running up and down its length continually, comparing it against the desired pattern

Ugh!These are called enzymes. Nanobots as normally pictured (a little robot with arms and pincers etc etc) are just pure science fiction. This is one of the worst areas of pop science literature.

This project is simply a lot of molecular biology, nothing novel in the techniques. What's new is trying to design a genome by hand as opposed to letting nature do it. I am skeptical that 1. it will work (beyond copying known genes), and moreover, 2. it will be even close to what evolution can/has accomplished.

What got kind of mushed together in the articles is a totally different aspect, that of non-natural amino acids. Peter Schultz;s lab (which is just down the hall from me) has created a system where a bacteria can incorporate an amino acid that is not one of the twenty used in natural proteins. You can add amino acids with all kinds of novel chemical groups and see if you can evolve proteins/organisms to work better with this expanded toolkit. Pretty cool.

-Ted

I don't see this. Mail-order gene synthesis [gene-synthesis.info] is still available with no restrictions. You can fabricate your own viruses that way.

Speaking as a molecular biologist who works with bacterial viruses, I'd like to quibble a bit about this. All the link you gave is to is a site that makes synthetic DNA sequences and puts them in a plasmid or phagemid vector. That has no relation to making a unique virus. Theoretically, I'd say custom-designing an AIDS-like viral disease vector from the ground up would take the full effort of about 6 people over 3-4 years & would require Biohazard Level 3 facilities to avoid killing yourself. A good Ebola-style killer is much more difficult because of the BL-4 conditions needed, probably needing almost a decade. Factor in even longer time frames if you'd like to invent a cure for this bug before you throw it out there, so you can keep your evil friends from dying.

DNA is just a chemical, and alone it just sits there. The DNA the company you linked to makes is not in the form of a viral genome, and therefore can't be a viral component. Assuming the DNA itself has the proper phage origin of replication needed to perpetuate in a virus, it still needs a good bacterial host and a "helper" phage of some sort to co-infect with it and provide the remaining genetic material, the genes encoding the proteins your DNA lacks.

Lastly, the main thing keeping biological weapons from being mass-produced is the fright level. The people with the knowledge of how to do this stuff know they can, with the design of the right agent, eliminate humanity. Most of these people are pretty smart and don't want to do that.

Current US-government research [nano.gov] is becoming more heavily funded by the military.

It always has been. DOD/DOE have always been big funders of research.

There's ongoing interest in a DNA reader

What, you mean like this one? Of course it's not nanotech, but you can usually get one for about 300K a pop. The ABI 3730xl DNA analyzer is the current state of the art in "DNA reading", and requires its own benchspace. Somehow I doubt I'll be doing high-quality DNA sequencing in my pocket anytime soon.

What application running under Windows 3.1 are people still running without upgrading -- I'd like to know!

In my experience, lots of Medical devices are still running off of Windows 3, DOS 6.22, or similar. Probably due to the computer being bundled with the $50,000+ device

Luckily, newer devices come with Windows NT and a seething mass of Oracle, Java, and homegrown code. The software corrupts itself every month or so, and doesnt work if you put a password on the Administrator account.

So as far as Microsoft OS controlled devices go, I prefer ones running on older operating systems to dumb to be cracked.

It will not replace conventional sequencing technology, unless it can beat the now pretty cheap cost. Conventional sequencing is based on labelling the individual DNA bases with a different flourescent dye, and running the DNA through a gel which seperates the DNA according to size: As each base runs through the gel, it goes past a laser/detector which can detect the specific DNA base (A,T,C or G) at that position. Due to gradual impovements to this technique over the last 20 or so years (originally it employed radiation, rather then flourescence) the speed, sensitivity and cost has decreased dramatically. For example, the human genome project started in ernest about 10 yrs ago. Celera Genomics, using modern technology (and alot of financial backing, and the fact they are a subsidiary of the people who make sequencing machines,) competed the genome in a matter of months. The increase in DNA sequencing capacity puts moore's law to shame.

For example, our lab could process around 100kb (thats KiloBases guys!) of data a day, but we never even touch this with our machine. No need, and the same stands for many small-medium research labs. Alot of people like us will probably stick with conventional sequencing technology for a long time (it works well, is high enough throuput, cheap & easy).

However, the are some exciting applications with single strand sequencing. For example forensics. Also, it allows the oppotunirty of sequencing RNA (this is the "messenger" which passes the "important" part of the DNA message to the ribosomes, which then "compile" a protein - the stuff which actually does things, like an enzyme or structural component). Sequencing RNA is exciting, as currently you have to convert the RNA back to DNA (which can cause problems) and then sequence that.

Another obvious application for this would be very high throuput sequencing which would be employed by the major sequencing centres. Yes, i know we already have the Human Genome, but a fashionable idea at the moment is comparative genomics. This is very much taking biology back to its roots (i.e. like Darwin and Wallace comparing the morphological characteristics of certain species and infering adaption), but at a molecular level. This will yield amazing insights with discoveries having important implications from medicine to evolution. In fact I think the general public & media will soon be bored of this. Each week it will be a new genome being announced; mouse, chicken, rat, pufferfish, rice, corn, dog, cat, cow, chimp......

It will not replace conventional sequencing technology, unless it can beat the now pretty cheap cost. Conventional sequencing is based on labelling the individual DNA bases with a different flourescent dye, and running the DNA through a gel which seperates the DNA according to size: As each base runs through the gel, it goes past a laser/detector which can detect the specific DNA base (A,T,C or G) at that position. Due to gradual impovements to this technique over the last 20 or so years (originally it employed radiation, rather then flourescence) the speed, sensitivity and cost has decreased dramatically. For example, the human genome project started in ernest about 10 yrs ago. Celera Genomics, using modern technology (and alot of financial backing, and the fact they are a subsidiary of the people who make sequencing machines,) competed the genome in a matter of months. The increase in DNA sequencing capacity puts moore's law to shame.

For example, our lab could process around 100kb (thats KiloBases guys!) of data a day, but we never even touch this with our machine. No need, and the same stands for many small-medium research labs. Alot of people like us will probably stick with conventional sequencing technology for a long time (it works well, is high enough throuput, cheap & easy).

However, the are some exciting applications with single strand sequencing. For example forensics. Also, it allows the oppotunirty of sequencing RNA (this is the "messenger" which passes the "important" part of the DNA message to the ribosomes, which then "compile" a protein - the stuff which actually does things, like an enzyme or structural component). Sequencing RNA is exciting, as currently you have to convert the RNA back to DNA (which can cause problems) and then sequence that.

Another obvious application for this would be very high throuput sequencing which would be employed by the major sequencing centres. Yes, i know we already have the Human Genome, but a fashionable idea at the moment is comparative genomics. This is very much taking biology back to its roots (i.e. like Darwin and Wallace comparing the morphological characteristics of certain species and infering adaption), but at a molecular level. This will yield amazing insights with discoveries having important implications from medicine to evolution. In fact I think the general public & media will soon be bored of this. Each week it will be a new genome being announced; mouse, chicken, rat, pufferfish, rice, corn, dog, cat, cow, chimp......

What really strikes is that Juno has brought in Yuri Rozenman, formerly of Applied Biosystems and with 13 years of experience in the bioinformatics field, to head up the project as vice president in charge of the Virtual Supercomputer Network. (source: here). The link between Applied Biosystems and informatics is the automation and analasys of genetical sequences
- this gives me the creeps - can you imagine ... collecting data on all those people

I got the following email from Nature:


Dear Colleague:
We are very pleased to offer all users of Nature's electronic services a
FREE sample of the May 18th issue of Nature. To request a free print copy
containing the Chromosome 21 paper, use the order form at:
http://www.nature.com/marketing/freecopy/
These free copies of Nature are produced with support from AppliedBiosystems -
http://www.appliedbiosystems.com
Forward this e-mail to let your friends and colleagues know about this
special offer.
Chromosome 21 is the second human chromosome sequence to be documented,
encompassing more than 33 million base pairs of DNA, and its publication
therefore marks a major scientific milestone. A striking feature of the
chromosome is that it contains less than 300 discernible genes. This implies
that the whole human genome may contain no more than 40,000 genes, many
fewer than previously thought.
The chromosome sequence reveals the organisation of a number of genes linked
to specific human disorders, and will speed the search for several more
disease-linked genes. The availability of this sequence will also provide
valuable tools for investigating the basis of Down syndrome, which is caused
by the inheritance of three (rather than the normal two) copies ofchromosome 21.
Yours sincerelyRichard GallagherBiological Sciences EditorNature