New Startup Hopes to Push Open Source Pharmaceuticals

waderoush writes "Nothing like the open source computing movement has ever caught fire in biology or pharmaceuticals, where intellectual property is king. But drawing inspiration from the people who make Linux software, and the social networking success of Facebook, Merck's cancer research leader has nailed down $5 million to launch a nonprofit biology platform called Sage, which aims to make it easier for researchers around the world to pool their data to make better drugs. 'We see this becoming like the Google of biological science. It will be such an informative platform, you won't be able to make decisions without it,' says Merck's Eric Schadt, a co-founder of Sage. He adds: 'We want this to be like the Internet. Nobody owns it.'"

Comments

push

[stoolpigeon]

i've found that there is plenty of pull, no need to push.

Pushers

[andrewd18]

I can hear it now: "We need these open-source drug pushers off our streets!"

Re:Pushers

[megamerican]

can hear it now: "We need these open-source drug pushers off our streets!"

These guys are too late. The CIA already did this with LSD!

Re:Pushers

[ILuvRamen]

and out of our inboxes! Can't forget that one. I mean everyone's thinking meth labs but do we really want the recipe and process out there for some prescriptions so people can make them in their basement and try and sell em online with the same stupid tactics we see today? I don't think the FDA would approve Billy Bob's Basement Joint Care Medicine - "made with open source information"

Yikes

[Anonymous Coward]

And therefore, no one is responsible for it? May work with software, but I think they're pushing it.

Motivation

[qoncept]

make it easier for researchers around the world to pool their data to make better drugs.

As in, like, paying them lots of money? No? I don't see this ever getting off the ground. And, uh, ask Proctor and Gamble what $5 million will buy you.

Re:Motivation

[Superdarion]

According to your ideas, then, Linux would have never got off the ground and yet here we are.

Not enough to do anything really.

[LurkerXXX]

$5 million?

That will be burnt up in a single clinical trial.

Re:Not enough to do anything really.

[jackchance]

Sage is not a research project, it will not conduct trials. it is a data-mining project. They idea is simply to create a standard API so that all the current research will be more effective. The $5M is just to get the thing off the ground. As soon as it has a single success, the funding will flow like water.

University Open Research

[Anonymous Coward]

You mean like when research was in the domain of the university, and when science was done by building on the prior work of others? The big dollar companies siphoned away the talent from universities and went patent crazy. They're the ones that started this in the first place.

The same can be said for internet technologies - people forget that fundamental web technologies such as web browsers and LDAP came out of university research, not out of the big companies or the major standards bodies.

Re:University Open Research

[Daniel Dvorkin]

Shhh! You're not supposed to talk about science and the sharing of knowledge! You see, these days it's all about Innovation(tm). Nobody's sure exactly what Innovation(tm) is, but we know it's heavily dependent on Intellectual Property(c) and it's vitally important that Intellectual Property(c) be Protected(r). How else are we going to synergistically leverage our core assets to maximize stakeholder value?

Re:University Open Research

[LynzM]

I'm dying over here... only because what you just said could have come verbatim out of my company's quarterly newsletters. It didn't used to be like this, there...

Re:University Open Research

[jc42]

Nobody's sure exactly what Innovation(tm) is, but we know it's heavily dependent on Intellectual Property(c) and it's vitally important that Intellectual Property(c) be Protected(r).

Actually, it's fairly easy (now that we have google as a research aid) to make a sampling of the use of the word "innovation" and determine its meaning:

innovation (n.): Making small, mostly cosmetic changes to someone else's product, then marketing it as an important new development, while suing the producers of the earlier product for infringing on your Intellectual Property in an attempt to bankrupt them with your larger legal budget.

The term is occasionally found with other meanings, but this is the primary definition that will help readers understand most of the uses they'll find today.

cool, but...

[token_username]

This is a very cool idea, but the stakes are a bit higher. I'd think there's going to be significant push-back getting used to the idea of drugs coming from a bunch of guys in their garages. It's sort of like if open source software started designing software for nuclear power plants.

Then again, maybe people are just so sick of drug prices...

Re:cool, but...

[Jurily]

drugs coming from a bunch of guys in their garages

As long as experts contribute, there shouldn't be a problem. Maybe a registration with credentials would be good.

Software is special, in that all the hardware required is now commodity, and all the knowledge can be accessed fairly easily. At least, you won't see $300 biochem labs from Dell.

Re:cool, but...

[mea37]

I don't see that anything these guys do WRT building an information platform is going to change the regulatory environment or layers of process (and expense) involved in actually bringing a product to market. So I'm not concerned about public perception of safety... but it does raise a different issue.

So this platform provides the basis for a new drug, and "nobody owns the IP" (sort of); ok, that means nobody gets the lock-in of being the one and only brand manufacturer of the drug for a few years after it gets approved. Then who's going to commit the time, money, and effort to getting the drug through the layers of testing and trials to become FDA approved? Who's going to take on the legal liability associated with marketing a new drug, when they can only command generic-level pricing?

If this platform discovers all of the otherwise-patentable innovations to create a new drug, I'm not sure how the drug will be brought to market. One possibility (assuming the model is less like GPL and more like BSD) is that the final innovation for a drug will come about in the traditional way, creating a faster pipeline of drugs that are still marketed as expensive brand drugs for the first years of their life. Another is that companies will specialilze in taking on the risk and expense of bringing an unpatentable drug to market, and the market will determine a premium above "normal" generic pricing (but hopefully below normal brand pricing) that they'll command for their effort. That latter approach could be sensitive to anti-competitive behavior, though.

Re:cool, but...

[Hordeking]

drugs coming from a bunch of guys in their garages

As long as experts contribute, there shouldn't be a problem. Maybe a registration with credentials would be good.

Minor problem. Who gets to determine that some researcher isn't an expert, as opposed to that biochem college dropout who knows what he's doing, as opposed to the well meaning schmo whose job is construction, but he knows some folk remedies, as opposed to a methamphetamine dealer whose knowledge of how to brew some rocks is exceeded only by his stupidity in smoking around ether?

Re:cool, but...

[budgenator]

Right now we know the human genome and that it's about 99% the same for everybody; if we know what the genetic differences are between people with cancer and those without, the differences in which genes are active, what the mRNA and proteins are doing, then we can attack the disease through those differences. Knowing the differences is just a stepping stone to creating safe and effective medicines, big pharmaCos are still going to be able to make money their old fashioned way with this data.

Even now anybody can go and poke around in Genbank over at National Center for Biotechnology Information

Re:cool, but...

[Bowling Moses]

"I'd think there's going to be significant push-back getting used to the idea of drugs coming from a bunch of guys in their garages."

How about from a bunch of guys working in a warehouse in one of the bad parts of town? I ask in all seriousness because a friend of mine is doing exactly this in a biotech startup and apparently attracting venture capital hasn't been too rough. Sure I kid him about being in the drug business on the bad side of town but nobody will ever really know if something looks promising enough to partner with a big company to push through clinical trials. In any report you'd probably just see the startup corporate name and logo (I hope my friend didn't draw it because then it'd be a cartoon chicken humping a moose or something) and "in partnership with MegaBuck$ biotech giant NASDAQ symbol ASDFAS."

Re:cool, but...

[Draek]

Just a question then: how do generics get made and sold? do they get a "free pass" from all that expensive regulation?

Plus I've always been told that the brand-name pharmaceutics are priced as such to pay for the billions being spent on research, and if a bunch of academics is willing to do that for free companies willing to make it shouldn't need Big Pharma pricing to get a nice profit, would they?

Re:cool, but...

[mea37]

Well, I can give a definite answer to one of those, and can only speak generally to the other.

A generic isn't so much a "new drug" as it is another manufacturer's vesrion of an existing drug. When the existing drug's patent expires, it's already through FDA approval, so generic manufcaturers can more or less pick it up and run with it as long as they follow certain rules about generic equivalence. (There are a couple different classes of generic, but the short form is "same active ingredients in the same dose; not necessarily the same inactive ingredients".)

By the time a drug can go generic, not only has the active formulation been approved, it's also been tried "in the wild" for some number of years. So even though they aren't run through their own full approval process, generics are historically safer from a statistical point of view. (Nobody's going to make generic Vioxx; that sort of thing.)

Now to your other question... I've never seen the books on a drug as it moves through the development pipeline, so I don't know the exact breakdown of costs. Pharma companies cite "R&D" as the cost driver of drugs in America; but (1) this project will only cover the R, not the D; and (2) the R&D explanation is probably only part of the story. When their spokespeople say R&D, it's a better-sounding explanation than "you're subsidizing drugs in other countries that regulate drug prices, and you're paying for our insurance and legal fees, and our ad budget".

Oh, please.

[chill]

Next thing they'll be telling us is we could GROW our own medications in gardens. Medicine and pharmaceuticals are *hard* and require a lot of big government seed money, research, lobbyists, more money, more lobbyists, advertising, etc. The idea that you could grow, say a drug to suppress inter-ocular pressure in glaucoma patients, or a nausea-suppressive for chemotherapy patients is patently absurd! I mean, what next? Analgesics from tree bark?!

Hippie, commie, open-sourcers will never learn.

Re:Oh, please.

[Anonymous Coward]

I would mod you insightful & informative, if I had the points.

Re:Oh, please.

[dkleinsc]

Next thing you know you're going to be suggesting that ordinary herbs are perfectly good for helping people sleep or combating migraines too.

Hippie, commie, open sources will never learn indeed.

Re:Oh, please.

[msuarezalvarez]

We all know that Merck is one of the last stands of hippie communism, of course...

Re:Oh, please.

[Anonymous Coward]

And I would counter that mod in a heartbeat. Thanks for playing.

Please stop touching me there.

Re:Oh, please.

[garett_spencley]

Well, we will never know how truly hard and expensive medicine is, since there's enough regulation in the industry to make new entry very difficult.

Of course drug research is expensive when you need to a) make sure your research is patented enough so that you have the exclusive rights to anything and everything that you research and b) make sure that you're complying with the expensive government regulations. Regulations that are pennies for a mega-corp but prohibitively expensive for a new start-up.

It's also common procedure for any big corporation to pay top dollar for retired politicians to lobby government in their in their favour. To regulate in ways that make it profitable for the existing corporations at the expense of everyone else.

Human history is full of small groups of researchers, not connected with huge pharmaceutical companies, who made important discoveries in medicine. From penicillin to the polio vaccine.

Re:Oh, please.

[Hatta]

Next thing they'll be telling us is we could GROW our own medications in gardens.

You could, if it weren't illegal.

Re:Oh, please.

[Hatta]

Let me fix those links for you:

Next thing you know you're going to be suggesting that ordinary herbs are perfectly good for helping people sleep or combating migraines too.

Re:Oh, please.

[dkleinsc]

I got the gist of the OP, but I thought it worth mentioning that perfectly legal stuff can also be useful.

Re:Oh, please.

[AlexBirch]

Don't forget biologics (using proteins instead of small molecules: read UCSF/Genentech) and siRNA.

Re:Oh, please.

[minorgroove]

My guess is that anything Merck would find useful (patentable) they would patent, and leave the rest for this open source project. GSK is doing a similar practice. Part of the motivation is to encourage development of drugs for neglected diseases, that is, diseases where the market is small and big companies like Merck and GSK have no desire to drop the millions to develop the drug that wouldn't help that many people, or would only help poor people.

Re:Oh, please.

[Yvanhoe]

And to suggest that it will take some hackers to fulfill the promises of genetically modified organisms (plants that produce medicines for instance) is just crazy talk.

The big OPEN SOURCE project that I see iseducation

[CrazyJim1]

If you believe in Sesame Street for kids, you should be interested in online education for adults. The reason why you can't do every subject known to man on television is that there is only limited air time and people would be uninterested in stuff they already know. But you can make an online education school which has videos of lectures for every level of education. Throw in some tests and written course(book) work, and you can guide people through education if they have the drive. You put in a lot of redundancy so there are many ways of looking at the same subject matter if it doesn't click with the student asap. And then you have a pay service where you can ask a teacher question through IM or email.

I don't know how to start this though. I considered being a jerk and just linking everyone's educational videos on a site that is just a giant index to start... But I don't want people complaining that it is their Intellectual property. The task is too big for me to tackle alone because even though you only have to make a years worth of videos one time for a subject, it still takes a lot of time to do this. To make an online education school with videos would take a lot of work, but I think it'd be worth it for society. Anyone have ideas on how to start something like this?

Drug Testing

[Anonymous Coward]

A major expense in the development of pharmaceuticals is the testing and approval phase. Only wealthy entities like corporations or governments can afford it. I don't see how the open source concept can get around that problem.

Re:Drug Testing

[mr_mischief]

It's easy. The big drug companies can fund the trials if they want to manufacture and sell the drugs. They can't patent the drugs if they get the research from someone else. The big question is whether the big drug companies would rather invest in the research and reap the reward of an exclusive market or if they'd be willing to fund trials and sell the drugs if they have to share the sales but also share the expense of research.

Re:Drug Testing

[Rich0]

Drug research isn't actually all that expensive (as in generating concepts). What is expensive is drug development - which is working a concept into a drug candidate and then putting it through trials.

I suspect that what will happen is that drug companies will look at the breakthroughs in these open consortiums and then develop candidates and patent them and run them through trials.

Example - the "open source" consortium discovers that inhibiting enzyme A cures cancer. Now, you can't patent the idea of inhibiting enzyme A. However, you can patent molecule 123 as an inhibitor of enzyme A. Somebody else could of course come up with molecule 456 which does the same thing but is a different molecule entirely. That's what we call a me-too drug and it is the reason why people with drug allergies don't die of diseases (they can take a me-too drug instead), and the reason for marginal improvements in classes over time (maybe molecue 456 is slightly better than 123).

However, once the company proves 123 is safe, they own the market until soembody else comes out with another drug. 123 is after all patent protected.

Consumers still win because maybe 456 comes along a year later and prices drop as they compete.

The issue at big drug companies is that they're having trouble coming up with breakthrough ideas for new drugs. The market doesn't need another statin that works 3% better than the 14 that are already on the market. However, something novel would certainly be both profitable and beneficial to the public. So, drug companies are trying to fund more novel R&D. Once some concepts worth developing come out the big pharma companies are experts at running molecules through the process, and after a few hundred million dollars spent getting something on the market.

This is also smart as the expensive part of drug development is the development part. You're not going to find poorly-funded researchers contributing much to that part of the puzzle. However, the blue sky research component needs ingenuity more than money - and that is what things like this are good at.

It is an interesting concept - I wonder how it will work out...

Re:Drug Testing

[tmosley]

A me too drug is more like a drug number 124, with some part of the molecule that doesn't interact with the site of interest is modified to give you TECHNICALLY new molecule. Patent is submitted, media machine is spun up, and your NEW purple pill hits the market, with the exact same effectiveness and side effect profile as the last one.

If it were an entirely different compound, it would just be another drug that treats the same problem. It might even do it in a different way.

Re:Drug Testing

[Rich0]

A me-too drug by definition has the same mechanism of action. For example, even though insulin and metformin both lower blood sugar one is not considered a "me-too" of the other since they have completely different mechanisms and potential uses.

Most me-too drugs usually aren't trivial variations on existing drugs. Sometimes antibiotics fall into this category (often to defeat some resistance mechanism).

I would think that a drug that is only a trivial variation of an existing drug would be risky from a patent perspective. Why spend hundreds of millions of dollars developing a drug that might be open to a challenge to its novelty? If you have the processes worked out for screening drug leads for a particular activity you might as well develop a more novel molecule if it is going to cost about the same either way.

If you have any examples of truly trivial changes in me-too drugs I'd be interested in seeing them. The only one that I can think of is Nexium/Prilosec. I think that granting a patent on that is a bit of a stretch - anybody skilled in the art would predict that a purified enantiomer would be likely to have double the activity of a racemic mixture. On the other hand, while lots of people get up in arms over that one I don't see much harm in it - people can always take double the dose of the generic racemic mixture and get the same effect for far less cost. If people want to pay 10X the cost for essentially the same clinical effect more power to them.

Authentication

[DoofusOfDeath]

If one gathers data from many sources, in order to justify to the US FDA some claim about a drug: how can one certify that those data are accurate?

I was under the impression that despite its horrific flaws, the current regime requires the drug researchers to seriously vouch for the (subset of) the data they present to the FDA.

Re:Authentication

[mr_mischief]

There was just recently a case in which the FDA quit accepting applications for approvals from a company. That company was found to be tainting studies, and was the only source of data for the drugs they wanted approved. See bio-medicine.org's coverage of that news item.

If you have multiple sources and most of them are reputable, are you better or worse off than having one source with a unique incentive to put their own drug in the best possible light?

Re:Authentication

[garett_spencley]

"I was under the impression that despite its horrific flaws, the current regime requires the drug researchers to seriously vouch for the (subset of) the data they present to the FDA."

Just like suing customers does not help the recording industry, killing customers is not in the best interest of the pharmaceutical companies.

There may be something to be said for drugs that treat HIV/AIDS, cancer and other diseases where the patient needs to be on medication for many years. There is also something to be said for addictive drugs and exploiting addiction to make a profit. A drug company that sells a drug that is promoted as a cure or a treatment but actually kills people or makes them sick is very bad for business.

There is a tremendous incentive for drug companies to not put out drugs that harm people. The public doesn't need FDA regulations to keep drug companies in check. We can do that ourselves through consumer watch groups, peer review and independent studies. Last I checked the government doesn't own our bodies. So responsible adults who wish to take risks in drug trials shouldn't need the government's permission to do so. FDA regulations, like almost any kind of government regulation, makes it extremely difficult for new competition by placing business (and consumer) decisions at the discretion of the regulatory body. It gives the big pharmaceutical companies a competitive advantage by limiting new entry into the industry. It plays a part in keeping drug prices high, along with patents (more government intervention that benefits a special interests).

So I think you raise a very good point. The FDA is probably what is going to prevent this project from accomplishing much.

Re:Authentication

[glwtta]

If one gathers data from many sources, in order to justify to the US FDA some claim about a drug: how can one certify that those data are accurate?

No, you gather data from many source to formulate the hypothesis that allows you to make that claim - to justify the claim to the FDA you do clinical trials as per usual.

Ambitious

[ieatcookies]

While I hope this works I have a hard time picturing the outcome not being tarnished, influence, and wrecked by profit. Like so many facets of R&D, the people doing the work are being paid to do so and the people doing the paying don't want to share.

$5M won't even keep the lawyers on retainer...

[AliasMarlowe]

Intellectual property may be king, but the lawyers are queens (pardon the expression), and their games are hideously expensive. You can't get into the legit end of the drugs business without a strategy for covering legal liability. You should budget at least as much for this as for clinical trials or production facilities. $5M is peanuts in this game.

Re:$5M won't even keep the lawyers on retainer...

[DoofusOfDeath]

...You should budget at least as much for this as for clinical trials or production facilities. $5M is peanuts in this game.

I'll work for peanuts!

Re:$5M won't even keep the lawyers on retainer...

[Dishevel]

...You should budget at least as much for this as for clinical trials or production facilities. $5M is peanuts in this game.

I'll work for peanuts!

I'll work for $5 Million

Re:$5M won't even keep the lawyers on retainer...

[ufoolme]

I'll work for peanuts!

ahhh... so how's that biology degree working out for you? :)

Already there in bioinformatics and genetics

[Daniel Dvorkin]

Open access journals such as those from BMC and PLoS, databases such as those at NCBI and EBI, software repositories such as Bioconductor and the Open Bioinformatics Foundation projects (Bioperl, Biopython, etc.) If Sage can take it to the next level, good for them, but I'm not sure I see how one group is going to accomplish this. I suspect it will have to happen more, um, organically, the way open access publication and biology-targeted OSS have.

Since we're comparing to software...

[Anonymous Coward]

Are we going to have crazy medicine patents too? Like patents for 'a substance, which can be put into in a (human) body, with the function to remove an (unwanted) organism from that body'?

It won't be long before a monopolistic medicine company will start threatening to sue patients for patent infringement.

Re:Since we're comparing to software...

[Anonymous Coward]

There already are. There are patents on taking two drugs at the same time.

Re:Since we're comparing to software...

[Anonymous Coward]

There already are. There are patents on taking two drugs at the same time.

Maybe putting two things in your mouth at the same time, counts as 'prior art'. Finally, the adult entertainment industry can help us.

Re:Since we're comparing to software...

[mea37]

???

The drug industry runs on patents today. You seem to be assuming that software today is more tightly patent-controlled than drugs today; you would have that backwards. (Not every piece of new software is covered by a patent.)

Re:The big OPEN SOURCE project that I see iseducat

[Anonymous Coward]

Although something of the scope that you describe certainly does not exist yet, there are projects along those lines. The main such projects I know of are MIT's OpenCourseWare, which apparently has spread to some other universities (Wikipedia page). In a similar, but currently much smaller project, Cornell has begun putting videos of some lectures online, but it appears to be only for Cornell students. Hopefully that will change.

Getting away from just college-level materials, there are a lot of collections of free textbooks, as revealed by a quick Google search (and remembering from prior Slashdot discussions on the topic), but I am not familiar with any of of them, so I do not know which ones are actually worth looking at. Specifically, the Wikibooks sister project to Wikipedia and its subproject (which I had not seen before) Wikijunior may interest you.

I am not sure how you feel about the MediaWiki projects, but that seems like a natural place to put in your efforts. If not, perhaps one of those other links may point you towards a project you are interested in helping with. Depending on how complete and high quality the existing material is, a better project might be one of making easier to find and encouraging people to actually use free educational materials, which could lead to more people contributing to those projects.

Not "open source pharmaceuticals"

[Ungrounded Lightning]

When I saw the title I thought "How the HELL can you have 'open source pharmaceuticals' in a legal regime where new drug compounds are illegal by default?"

Then I read TFA.

This has NOTHING to do with making "open source pharmaceuticals". This is about sharing data among drug companies and doctors to try to get a better handle on things like:
  - understanding the gene-regulation changes that occur in major diseases
  - designing better drugs using this data
  - customizing drug therapies by selecting drugs that are a good match for a patient's genetics and disease, picking those that will be safe and effective for him in particular while avoiding those that would cause dangerous side-effects due to his particular genetics.

It looks like it will run afoul of HIPPA unless it's very carefully designed.

BAD article title. No donut.

Re:Not "open source pharmaceuticals"

[Daniel Dvorkin]

HIPAA (not "HIPPA") doesn't have to be a barrier to sharing research data -- take a look at the U. of Pittsburgh's Honest Broker System for a very nicely put-together, largely decentralized method of moving data around while staying well within privacy guidelines. Financial interests are a much bigger obstacle to the free exchange of knowledge than are even the strictest regulations.

sage

[Anonymous Coward]

sage for not being GPLed... fucking fascists

Possibly worse than that

[Weaselmancer]

What if a patent troll pharma company just reads the site and applies for patents on everything posted there?

Re:Possibly worse than that

[Daniel Dvorkin]

Hopefully at that point, prior art kicks in. Whether it would actually work that way in practice, of course, remains to be seen.

Re:Possibly worse than that

[Weaselmancer]

Yeah, prior art would kick in - but you have to have somebody who cares enough to hire a lawyer and argue that point. And that means money.

And if nobody does fight it right away, if the patent troll gets in a first win, it gets much harder to prove your prior art case.

See Jeff Bezos for more on the topic.

Re:Possibly worse than that

[mea37]

Having a published repository of the data, presumably with dates and citations to show authorship, is actually one of the best defenses against a patent troll scenario.

Re:Possibly worse than that

[AlexBirch]

Those companies are called generic pharmaceutical companies. They'll bring law suits if there isn't prior art.

very intriguing

[Presto Vivace]

I will be interested to see where this goes.

Re:i have a startup idea

[Anonymous Coward]

a new kind of social network.

I predict that...

[__aaclcg7560]

Bob Dylan's "Everyone Must Get Stoned" will become the theme song for this movement.

Re:I predict that...

[KingAlanI]

Bob Dylan's "Rainy Day Women #12 & #35." will become the theme song for this movement.

Fixed that for you.

Open source computing in Biology

[Adam Hazzlebank]

Nothing like the open source computing movement has ever caught fire in biology or pharmaceuticals

Informatics for Biology... Bioinformatics. Is RUN by open source software. BLAST http://en.wikipedia.org/wiki/BLAST ,one of the most important Bioinformatic tools ever written, is public domain. It's paper is one of the most cited of the past 30 years http://archive.sciencewatch.com/sept-oct2003/sw_sept-oct2003_page1.htm . Bioinformatic clusters almost universally run Linux. Almost all popular tools are written by academics and supplied under open source licenses. To the degree that I'd say closed source software finds it hard to break in to this area, not the other way round. This is not only true of Bioinformatics, but also large scale Protein simulations. Namd p://www.ks.uiuc.edu/Research/namd/ is also available under and open source (though more restrictive than GPL or BSD license). And is one of the most popular Molecular Dynamics codes available.

Re:Open source computing in Biology

[Hatta]

It's a real shame, there's a big gap in the open source bioinformatics tool kit. There's no open source sequence analysis software that can conveniently do things like retrieve genbank entries from the NCBI, retain all features, search for primer sites and restriction sites, and then draw a map of it. There's none that you can use to simulate a restriction digest and ligation for in silico subcloning.

I've been using Vector NTI for this, and it sucks, but it's free (as in beer) for now. Later this year, they're killing the free license, I don't know what I'm going to do then.

Re:Open source computing in Biology

[fotbr]

Three options:

A) You pony up for a license, like they want.

B) You find something else and pay for a license.

C) You figure out some way to get some funding together - I'd suggest a university with good contacts in the so-called "science-friendly" Obama administration (Its only been a few weeks, we'll see how science friendly this administration turns out to be) and put together a better open-source alternative.

Either way, the tool has limited use, so it will require money, even for the "free" options.

sage

[Anonymous Coward]

sage goes in all fields? no, wait... wrong forum.

Not about making drugs, it's about sharing data

[neveaire]

What's interesting about this (I think) is that they're trying to open up research data that usually gets discarded or hidden. They're not necessarily talking about clinical trials of drugs in the FDA approval process. There's lots to be learned from the effects of drugs on various cell or tissue types at various stages of disease or age or any other variable of interest.

If a research group is studying the effects of compound A on some disease (atherosclerosis, for example), they might use a microarray study the effects of the changes in gene expression on endothelium. Maybe that compound turns out to be useless in this context, but they have data that might be meaningful on some other pathway like cell adhesion which is often implicated in cancer. That data would have been tossed because it was uninteresting to original question but could be meaningful to someone looking at something else.

But now you have two bits of information. Compound A doesn't effect atherosclerosis but it effects cell adhesion. And that tells us something about the wiring of the cell type in question. In their view, the interaction of genes forms a network and hitting one part of the network has an effect on cell adhesion but not atherosclerosis. So those pathways must not be directly linked. But compound A hits something in the cell adhesion subnetwork.

With a lot of little stories like this, you could build yourself a detailed idea of how different aspects of cellular machinery interact. And what targets are good to hit and what aren't.

I get the joke

[unifyingtheory]

because I'm in pharmacy.

Many drugs DO come from natural sources. example:
Pilocarpine: glaucoma drug "obtained from the leaves of tropical American shrubs"

Of course you couldn't extract and purify the compounds yourself. No one has a lab in his basement. Right??

Re:I get the joke

[budgenator]

Why, just smoke a joint every once in a while and forget the lab.

Re:I get the joke

[zeropointburn]

This turned into a book. Sorry. This post lacks citations and specifics for reasons that should become clear. A full-fledged fully-stocked bioengineering lab isn't really necessary. A high school chemistry lab would be overkill for most of it. Most plant extractions can be done with nothing more than an acid (hydrochloric preferred), a base (sodium hydroxide preferred), distilled water, a separatory funnel and a set of mason jars. Some extractions might further require a bunsen burner, while others might require an alternate solvent such as ethyl alchohol. A blender and a freezer is helpful. Anyone that has passed a lab course should be able to extract aspirin (and a bunch of other chemicals) from willow bark in their kitchen. Purifying it down to a single active ingredient is much more complex, but that step is often unnecessary. Provided the plant has no materials with higher toxicity than the sought-after chemical, a simple extraction can be done relatively easily. It takes at least a week, usually more like 4 weeks, so this isn't a 'pick that from the garden and extract' process. Actually purifying these extracts is generally either a crystallization or gravity separation process (or both), both of which can be greatly enhanced by the appropriate solvent or by the use of a centrifuge. There are some plants that contain other, unwanted toxic materials with similar physical and chemical properties. This is where the difficulty level starts to ramp up. If you know what you are doing, you can cause either the desireable or the undesireable substance in solution to react and precipitate out, then continue the refinement as normal. All that is required here is access to the appropriate reagents and an understanding of which chemicals to use (in addition to lab process familiarity). A person could become competent at all of these processes given a few hours' training and a guidebook with specific instructions. It would be no more difficult than passing a Red Cross first aid test. They would not be chemists, but they would be able to make useful medicinal plant extracts. Of course, this would never happen. The same skills allow access to a number of interesting compounds which are illegal, where the source plant is not (due to proliferation).

Re:I get the joke

[zeropointburn]

Noob mistake and karma burn. I forgot to post as plain text. My apologies.

This turned into a book. Sorry. This post lacks citations and specifics for reasons that should become clear.

  A full-fledged fully-stocked bioengineering lab isn't really necessary. A high school chemistry lab would be overkill for most of it. Most plant extractions can be done with nothing more than an acid (hydrochloric preferred), a base (sodium hydroxide preferred), distilled water, a separatory funnel and a set of mason jars. Some extractions might further require a bunsen burner, while others might require an alternate solvent such as ethyl alchohol. A blender and a freezer is helpful.

  Anyone that has passed a lab course should be able to extract aspirin (and a bunch of other chemicals) from willow bark in their kitchen. Purifying it down to a single active ingredient is much more complex, but that step is often unnecessary. Provided the plant has no materials with higher toxicity than the sought-after chemical, a simple extraction can be done relatively easily. It takes at least a week (without good equipment), usually more like 4 weeks, so this isn't a 'pick that from the garden and extract' process.

  Actually purifying these extracts is generally either a crystallization or gravity separation process (or both), both of which can be greatly enhanced by the appropriate solvent or by the use of a centrifuge. There are some plants that contain other, unwanted toxic materials with similar physical and chemical properties. This is where the difficulty level starts to ramp up. If you know what you are doing, you can cause either the desireable or the undesireable substance in solution to react and precipitate out, then continue the refinement as normal. All that is required here is access to the appropriate reagents and an understanding of which chemicals to use (in addition to lab process familiarity).

  A person could become competent at all of these processes given a few hours' training and a guidebook with specific instructions. It would be no more difficult than passing a Red Cross first aid test. They would not be chemists, but they would be able to make useful medicinal plant extracts. Of course, this would never happen. The same skills allow access to a number of interesting compounds which are illegal, where the source plant is not (due to proliferation).

Uh.. oh.

[Anonymous Coward]

Tag: abouttobedisappeared.

But seriously, you can bet none of them will be happy over this.
These guys are worse than software companies and music companies combined.

They'll rip your eyes out your ears just for taunting them...

I find it humorous that the captcha was "spoilers".

Cigar / cigarette business

[Anonymous Coward]

>There is also something to be said for addictive drugs and exploiting addiction to make a profit.

You seem to have forgotten our lovely little cancer promoters.
Even putting pictures of peoples rotten lungs on them won't put the junkies off them.
Sadly, addiction wins over image in this case.

I say create a virus to target nicotine and kill, i'm sure that will freak them out!

Re:The big OPEN SOURCE project that I see iseducat

[CrazyJim1]

Thanks for your information. I'll have a look at some of that stuff especially the free text books. The price of free is the development time, but the rewards are invaluable when complete.

won't happen for awhile

[circletimessquare]

hobbyist computers: couple hundred bucks
hobbyist biochemistry: millions of dollars

penalty for screwing up a computer project: reboot
penalty for screwing up a biochemistry project: chemical pneumonia, sterility, cancer, death, homeland security minions tossing teargas canisters into your window and barking orders

once upon a time, you needed a studio system to make a movie. now a teenager can make a feature length HD movie with his friends. nothing remains too difficult and too expensive forever, and someday, teenagers will be able to hack biochemistry in their basement. but the technological burdens are a little high right now

OTC...

[kabocox]

Screw this idea. I just want a few million people to pressure the FDA to make more known drugs over counter drugs rather than requiring a doctor visit. My kid had strep throat last week. My wife has it this week. We'd much rather go to walmart buy what ever the antibiotic or box labeled take this for strep throat rather than the system we have now.

For new drugs or unknown experimental crap our existing system is great. For getting drugs away from requiring doctors and where any mom can decide to buy it and give it to their kid, our entire outlook drugs needs to change a little.

I know for a fact that I wouldn't want to test any "new" drug on my family. I also know that I have no problems giving any of a variety of kids medicines to my kids or taking equate pain reliever when I feel that I need it. Heck, I feel that's great that I can take a pill and not have allergy symptoms for 1 day without having to go through a doctor. Why couldn't we have had that 5-10 years ago though?

For dangerous/lethal or very addicting drugs, sure keep them requiring a doctor, but for anything a doctor routinely will gives out to folks to use where they need to follow simple directions, why can't we start making our own decisions abit more? Hmm. It's our health at stake not theirs.

Re:OTC...

[robkill]

Very Simple,

If antibiotics are over-the-counter, then they will be over-used, and/or misused in ways that lead to more antibiotic resistant strains of bacteria (e.g. penicillin-resistant gonorrhea, or MRSA). Shelf life is another concern. Several common prescription medicines not only become ineffective as they age, but eventually become toxic. OTC interactions with prescription drugs are a common problem that would spread as more medicines are made OTC. Too many people take dosage and usage directions for prescription and OTC drugs too lightly as it is. Making more drugs OTC will only make this problem worse.

Re:OTC...

[Daniel Dvorkin]

We'd much rather go to walmart buy what ever the antibiotic or box labeled take this for strep throat rather than the system we have now.

The level of insight and understanding in this sentence demonstrates beautifully why antibiotics should never, ever, ever be OTC.

Sage -- a non-profit biology platform

[gringer]

Not to be confused with the non-profit maths platform, also called Sage.

This brings back morality to pharmaceutics

[Anonymous Coward]

Think about a researcher who unintentionally finds a possible cure for a disease but his employer decides not to develop drugs based on his results because e.g the potential market is too small or the investment costs are too high.
Isn't it irresponsible to lock up these research results forever, while someone else could continue this work to save lifes?

Existing non-Patented Drugs

[Herkum01]

I wish they would invest more time in making available drugs that have already had their patent expired. I am not talking about stuff that expired yesterday, I am talking about stuff that been out for years but the market is too small for a large company to invest in it.

I forgot the name of the drug, but it was a cheap drug that served a small market, but it very vital. It was being produced cheaply for years from one factory that served the whole market. Somebody bought it and then jacked up the price by 100 fold. Why? Because no one was going to bother with drug that had such a small market share, but it was critical the people who depend on the drug.

Someone tell me what the drug is? I believe there was an article in the NY Times a few years ago about it.

Re:Existing non-Patented Drugs

[Atario]

Vital but unprofitable? Sounds like a job for The People -- which is to say, government.

Bad analogy

[tepples]

According to your ideas, then, Linux would have never got off the ground and yet here we are.

Bad analogy. Linux is information technology; Sage is drugs. National governments regulate drugs much more heavily than IT.

Re:Bad analogy

[Trails]

A good analogy. Linux is IT, Sage is data collection and sharing.

What I'm trying to find, and more relevant, is if Sage's open source license will be "viral", à la GPL.

How is this different from already existing tools?

[virtualXTC]

Doesn't the NIH already do this with Entrez ? Plus there are plenty of data generating institutions that actually chave such infastructure such as Connectivity Map, Chembank and the personal genome project to name a few. From the article I'm having trouble seeing how "Sage" will offer anything unique.

Re:i have a startup idea

[Anonymous Coward]

I sure both of your trailer-trash moms are doing that quite effectively on their own.

I was wondering when this would happen

[RexDevious]

After all, the idea of open source (FWIK) was wanting something important to come in to being *more* than wanting to make a profit from the process. How many people have spent countless hours doing this so they could have an OS or DB that put "working well" before "being profitable"?

It seems to me that being treated or cured of a painful disease or condition ought to be right up there with not having to use closed source software (some would say I'm being redundant).

Drug companies are *companies*. Their first priority has to be profit, or they will be taken over by a different company willing to put profit first. But what good does that profit do if you make billions helping old men get boners... and then find out you have cancer? (hint: not a lot).

Normally when rich people get an incurable disease, they leave all their money to some institute trying to cure it. But it's a little late then, particularly if the institute they set up or funded puts a monetary barrier in front of anyone who'd want to help them. So yeah, someone out there is eventually going to have both the time and resources to put quality over profit.

I do hope the new drugs they come out with are a bit easier to use than those early Linux distros then. I hate reading long manuals when I'm sick.

Not ANOTHER Sage

[Anonymous Coward]

There are already a quadrillion different things named Sage. Many of them project within the science domain. May I suggest the name it Sage 2, or Sage 3?

Nobody owns the Internet?

[martas]

'We want this to be like the Internet. Nobody owns it.' I think he means 'We want this to be like the Internet, where people sell DRM'd information.'

Wikipedia, perhaps, would've been a better comparison.

Thank you, I'll be here all week

[Anonymous Coward]

Why don't they pool their drugs to make better data?

Could be the opposite

[jlebrech]

Don't opensource drugs exist already, aren't they called generics?

Some company could develop DRM'd drugs that check the colour of the box they are in.

If its plain white, you're screwed.

It is called ...

[steinbeck]

As we learn from this rather poorly written article over at xconomy, "Biology has never really had a social-networking movement like open-source computing, where thousands of loosely-affiliated people around the world pool brainpower to make better software". If you translate that into what was needed for biology (or chemistry) according to the xconomy author, it would translate into a "social-networking movement where thousands of loosely affiliated people around the world pool brainpower to make better biology". Now, I leave it to you extremely bright guys out there to figure out why I think that already exists and how it is called. And even when you see it from a more IT-centric perspective, biology (in contrast to my own field, chemistry) has been at the forefront when it comes to data sharing, open source and open standards.

Re:The big OPEN SOURCE project that I see iseducat

[Rue C Koegel]

there are how-to sites out there like this... find one thats free, as in open-source and non-profit, and encourage them to organize not only how-to PDFs and Vids, but quarterly class curriculum as well.

i homeschool my kid via WAVA.org, a washington state public school that uses K12.com materials... it's really the best way to teach a child, by far... so long as there's a learning coach with the patience to teach the child daily, for free. anyhow, there's no reason a sustainable non-profit version of k12.com's material couldn't be developed--and for a wider age group than just K-12th grade.

brainpop.com is another for-profit that could use an open-source non-profit retrofit!

Re:The big OPEN SOURCE project that I see iseducat

[Rue C Koegel]

i forgot about MediaWiki's WikiBooks... i suppose the smart thingto do here is generate a WikiSchool.org that incorporates wikipedia and wikibooks materials, along with hosted educational vids, into a curriculum to be followed by those seeking educational enrichment.

then those courses could seek qualification as accepted by the board of education, and a third party org could be developed--like WAVA.org--to monitor and provide proof of the success of students (accreditation of materials/course structure and educational oversight for the student body).

a free, open-source, Alternative Learning Environment for all!