Open source web sequence/plasmid viewer/editor components?

[Marc Juul]

I'm making a list of web-based plasmid and sequence viewers and editors.

Filters:

* Must be open source

* Must be client-side web

* No flash/plugins

So far I've found:

* AngularPlasmid: http://angularplasmid.vixis.com/
* GENtle2: https://github.com/Synbiota/GENtle2

What else is out there?

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marc/juul

[Jeroen Delcour]

https://benchling.com/

I've used it and found it a little clumsy and cramped but works fine.

[Jérôme Lutz]

Well, not open source and made to recommend genomecompiler use but it has a nice interface: http://www.genomecompiler.com/plasmid-viewer/

Why not make a holistic table, including all open and closed source viewers? 

Would you mind sharing the list with us? I'd love to put it on www.synbio.info in our software section. 

[Cathal (Phone)]

I'm seconding Marc that Open is crucial. Secret-innards software has no value to me and has no place in the scientific process.

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Sent from my Android device with K-9 Mail. Please excuse my brevity.

[Jake]

> Open is crucial. Secret-innards software has no value to me and has no place in the scientific process.

I'd counter that an exaggerated sense of entitlement and open bigotry like this have no place in science.

When someone takes the time and effort to create something for you to use for free, you have no business criticizing the author's choice of license to release it under.  Nobody's forcing you to use it.  To go so far as to then insult them by saying they have no place in science is really offensive.  Having such poor manners is what really has no place in science, and you will go nowhere in it with that attitude.

[Bryan Jones]

While I like open source as much as anyone, I have to agree that it's kind of silly to say that closed source software has no place in science. Should scientists be disallowed from using Windows? If you are doing processing of the sequence (e.g. A multiple sequence alignment) then it's important to know the math that goes into it, but it doesn't really matter if they don't tell you the way that they render the graphical drawings of a plasmid.

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[Raza]

RE: Open source discussion - Well, understanding what you have been doing and being able to communicate it adequately to others are virtues within science, so it's not quite like the choice of a more vs less transparent license is a scientifically neutral personal preference. 'Not being forced to use it' may mean that program authors have not committed a general moral offense, that that bar sits a lot lower than the one where a choice of method over its obvious alternatives is adequately justified to the scientific process. There are a lot of ordinarily-perfectly-polite things one can do that have no place in science, really.

All else being equal, I'd say say open source deserves to be a gold standard for scientific applications. Saying that writing and using applications under other licenses has 'no place in science' is hyperbole, I'll give you that, but along the same dimension I think that using harder-than-necessary terms to encourage preferred practices under scientific ideals falls some distance short of 'exaggerated entitlement and bigotry'.

[Cathal (Phone)]

More like "Should scientists be allowed to redact portions of their materials/methods chapters".

This isn't about the license, though asa separate issue I firmly believe that proprietary software is harmful to users' freedom and self-determination. Ignoring the liberty of scientists, is a piece of software were proprietary but the source code were available to all for inspection (which is *not* considered "open"), that would still be barely, slightly acceptable to the scientific process.

When the source code remains secret, then an entire section of the scientific process is sliced out of peer and piblic review, effectively a black box we're all supposed to trust. And, to replicate work, downstream scientists are also supposed to trust it, too.

Even when the workings of that black box are supposedly transparent ("It just pastes the sequences together!") it's as unacceptable to a scientific ethic as saying "I just extracted teh DNA": the methods matter to the scientific process and legacy.

So, yes: secret processes and methods have no place in science. Whether a crappy secret miniprep protocol or a crappy secret software platform.

...and if it's not secret, I still say reject if if it's proprietary, but that is a separate disussion riddled with human rights and general ethics questions, not a pure scientific process question.

[Koeng]

I think that equating "It just pastes sequences together" to "I just extracted teh DNA" to be flawed logic. Saying "the cloning was simulated with snapgene 3.1.2" is just about as good as saying "the DNA was extracted with the Qiagen miniprep kit", in which the latter is sufficient for a user to go and find out how the protocol was done (and vice versa). When a miniprep is done with 2 different kits, the outcome can be very different. When I paste sequences together, it doesn't matter if I did it in snapgene, GENtle2, notepad, or vim. All give the same outcome. To replicate my work, you can even do the cloning by hand for all I care, all I need to give is primers and sequence, which are both in text format. Putting DNA through proprietary software won't change the inherent text in anyway so that I couldn't replicate them in free open source software. It's just quicker.

I love open source software, and would jump to using it if there was a good alternative. Both the above open source softwares mentioned either 404ed or haven't been updated in months. Meanwhile, if I find a pragmatic issue in above mentioned proprietary software, I can email the support team, get a reply back in an hour, and get the fix within a week. This allows me to focus on experiments rather than coding software. 

It's not worth my time to figure out software to efficiently simulate cloning of DNA because the outcome is the same. I fully agree, if the outcome is changed by math involved, it ought to be open. But cloning with snapgene, benchling, genomecompiler, ApE, or any other proprietary software doesn't do anything different than cloning with GENtle2, AngularPlasmid, or DNApy. I care more about doing science than I care about the license of my software that does one thing. Is that really a bad thing?

-Koeng

[Nathan McCorkle]

On Sun, Apr 17, 2016 at 10:45 AM, Koeng <koen...@gmail.com> wrote:

I think that equating "It just pastes sequences together" to "I just extracted teh DNA" to be flawed logic. Saying "the cloning was simulated with snapgene 3.1.2" is just about as good as saying "the DNA was extracted with the Qiagen miniprep kit", in which the latter is sufficient for a user to go and find out how the protocol was done (and vice versa).

Blackboxing is fine if there is no alternative, but I would say there should be effort to actively try and 'unbox' these items/processes. The mini-prep might have been discovered by academics, published on, then improved by commercial industry... only to later be dissected by academics again when they were trying to improve/reverse-engineer things. (the reverse-engineering effort is supposed to be saved by patent disclosure... but... well... we all know those have their issues in practice and in society)

Science is definitely about being open and well documented, so things can be reproduced. Good, well quality-controlled black boxes can still fit in to this pipeline and accelerate the time-to-success of an experiment.

 

When a miniprep is done with 2 different kits, the outcome can be very different.

Which can be a MAJOR problem if the company that produced a closed-source/blackbox kit goes bankrupt or gets bought by another company that then discontinues that kit with no alternative. For all we know, the magic "spells" in children's cartoons that call for "frog extract" could have actually worked, at some historical time with some historical and specific frog and a specific extract technique. For the present-day though, this is just a junk recipe that we all "know" is fake/fictitious. (will the biochemists who did their PhD dissertations on magic frog-guts extract please stand up!)

I think the big difference, as a scientist/engineer is whether the solutions available meet my needs. As a decent programmer (and so called software engineer, by day, these days) I can tweak software to add new features sometimes within minutes of getting the source code. This is not happening with any decent commercial software tool through feature requests unless you've got thousands of dollars on the line and are willing to make it well worth their time. Pretty much the same thing about new features that are specific to your workflow, or maybe are experimental ideas. Another issue which I can attest to is, what if you have some technique which doesn't integrate with existing closed-source tools, and which you cannot even PAY the closed-source company to help you with, because you don't want to risk leaking ANY details about your own Intellectual Property.

I was just tweaking some open-source scientific simulator GUI code last night, it felt really good.

[Jake]

All else being equal, I'd say say open source deserves to be a gold standard for scientific applications. Saying that writing and using applications under other licenses has 'no place in science' is hyperbole, I'll give you that, but along the same dimension I think that using harder-than-necessary terms to encourage preferred practices under scientific ideals falls some distance short of 'exaggerated entitlement and bigotry'.

My statement may have sounded harsh, but it's not hyperbole.  I didn't make it to be mean, but I stand by it as a point of fact.  Cathal seems to feel he's automatically entitled not only to the fruits of someone else's labor, but also the process, underpinnings, and art involved in producing it.  All with the implied threat of criticism of that process and work.  That's not a constructive attitude, and it clearly discourages, rather than encourages, open source.

Bigotry is also the correct term to use for this attitude.  He has no empirical basis or support for his position, at least that we've heard, yet has a loudly voiced "intolerance toward those who hold different opinions from oneself."  He's advocating the attitude that closed source works are not appropriate for the purpose they were intended, essentially telling the authors that their efforts were worthless and even wrong, all based on his unsupported opinion.

I don't think the group should tolerate intolerance.  That is my specific critique of this attitude.  The sense of entitlement will cure itself though experience.

I'm a strong supporter of open source, much stronger than anyone else here.  I've written and worked on a couple open source projects before.  I've also threatened litigation over license violations before and achieved compliance, e.g. release of source code.  But there's absolutely no reason to be intolerant towards closed source.

This "leave the room because you're not welcome here," attitude towards useful programs that have contributed greatly to science just because they're not open source is simply ugly and counterproductive.

The other arguments seem like potentially valid concerns, yet they don't really hold their water very well with no empirical basis.  At best, they are an argument for how open source could potentially mitigate some hypothetical concerns, rather than any valid reason to avoid closed source software tools.

When software authors see intolerance and entitlement arguments as presented here... it quickly and effectively turns them off open source completely.

Imagine a cook with a customer who demands the recipe and to observe the preparation methods.  They argue that because they have eaten the dish they are entitled to the list of ingredients.  They want to see everything, including the preparation methods, based on the accusation that there may be some poison somewhere in the secret sauce.

Who in their right mind would comply with this?  Is the asinine customer going to stop if you give in and release your secret recipe?  Or are they going to proceed to criticise each and every ingredient and method?  When you demand, insult, cast suspicion, and threaten to boycott and slander someone's product... human nature is for them to give you the big FU, dig in their heels, and prepare for battle.

Hopefully we can be more constructive and tactful in the future, and observe standard scientific decorum when you ask for a "gift", regardless of whether your request is granted.

[Cathal (Phone)]

> Cathal seems to feel he's automatically entitled not only to the fruits of someone else's labor, but also the process, underpinnings, and art involved in producing it. All with the implied threat of criticism of that process and work.

You literally just described peer review.

[Jake]

> You literally just described peer review.

Maybe you should start your own journal and appoint yourself chairman of the peer review committee.  Then you can demand the firmware source of every thermocycler, timer, transilluminator, imaging system, thermostat, etc..  In a few years, when you've accumulated a few 800 page papers that meet your standard, you can publish your first issue.  I'm sure it will be a big hit.  ;)

Don't forget to include things like diagrams of their heating and lighting systems, lighting frequency, color temp., mechanical details of every cog and wheel in any timing devices used, and so forth (obviously source code for any digital devices).  You might find it hard to get details on the etching masks for every IC used in these devices, but you certainly can't publish something without these details.  The ICs could be discontinued and you'd have to etch exact replacements to have any hope of the perfect replicability we are now demanding.  Perhaps with special permission and unanimous consent of the review board you could allow logic diagrams to substitute in certain cases, as long as the complete datasheet is included and the functionality has been independently verified.

Perhaps with your strong leadership on this issue we can get rid of all these garbage papers with poisoned secret sauce that are currently being published.

[Koeng]

I think that he's simply pointing out the hypocrisy that everything experimental is peer reviewed while software is usually not. That is not a ridiculous thing to ask, what is ridiculous is to strawman this simple argument to the point of sarcasm. 

Anyway, this should be topical to the original poster's desires. So far, it doesn't look like there is any software which meets all qualifications. Are there any open source plasmid editors that are locally run? I tend to trust these more than browser based. 

-Koeng

[Nathan McCorkle]

On Mon, Apr 18, 2016 at 2:44 PM, Jake <jake...@mail.com> wrote:

Don't forget to include things like diagrams of their heating and lighting systems, lighting frequency, color temp., mechanical details of every cog and wheel in any timing devices used, and so forth (obviously source code for any digital devices).  You might find it hard to get details on the etching masks for every IC used in these devices, but you certainly can't publish something without these details.  The ICs could be discontinued and you'd have to etch exact replacements to have any hope of the perfect replicability we are now demanding.  Perhaps with special permission and unanimous consent of the review board you could allow logic diagrams to substitute in certain cases, as long as the complete datasheet is included and the functionality has been independently verified.

I'm pretty sure this is what is required of any military equipment contracts. They definitely check things like IC masks for something as high-level as a jet fighter. Whether they do so for all sub-systems, probably not, but anything critical I bet for sure. 

For the rest of us, there's #homecmos and resources like opencores.

[Jake]

Sure, I get what he's trying to say.  It's the intolerance, attitude, and level of review that I think is inappropriate.  What he's demanding goes beyond the details of how the data is manipulated, even beyond the exact bitwise manipulations of the data.  He thinks that the entire source is required, or else it should be prohibited from scientific use altogether.  This is analogous to demanding the details of the cogs and gears involved in a mechanical timer.  I could tell you that one revolution is equivalent to 60 min. +/- 3 sec..  But that's not what he's asking for.  He's asking for the exact details of how that result is accomplished, and that is what makes his argument absurd and deserving of sarcastic rebuke.

This entire argument has no place in science because there's one side that has no empirical support.  Closed source software is routinely used in science at all levels, and I am unaware of any instance where replication failed, or an invalid conclusion was reached, because of poison in the secret sauce, insufficient details of the algorithms used, or anything along those lines.

Any good scientist will use all the tools at his disposal, and valid solutions reached by any means can't be disregarded simply because of intolerance towards the means used to obtain them.

[Nathan McCorkle]

Though the military might not ask for the metal foundry process recipe... but rather they may have a very stringent quality-control checklist that any item must meet (which is a constrained black-box).

[Jake]

Sure, and if discrepancies or outright fraud were involved then it would be appropriate to try and drill down to that level.  It would still be far easier to just compare black box X results with open source Y solution to validate or discredit the result.

It would be nice if science got a substantial fraction of what the military does, but even then it would be unfortunate to squander it on unimportant minutiae like this. 

[William Beeson]

I think this post has gotten far off the tracks of what the OP was asking about.  On the topic of open/closed source software and science -- I don't think software that is "closed source" should be published upon.  For instance, if I had developed a new algorithm and software package to assemble DNA and wanted to publish that in a journal it should be required that the source be open.  However, there is nothing at all scientific about a plasmid viewer or web sequence viewer.  It is a general productivity tool which basically amounts to "looking at something on a computer".  It's no different than a program like excel or powerpoint or photoshop.  

If Cathal was referring to the first scenario, that is a very mainstream viewpoint.  If Cathal believes that the only software used in science should be opensource freeware, that is far away from the position of most scientists I have worked with.