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Comment Re:I still don't want it (Score 1) 280

Its built-in linux-like commands don't appear to work as expected, I guess due to aliasing. "ls" is fine. But with any arguments, and I get stuff like this:

PS C:\mingw\bin> ls -l
Get-ChildItem : Missing an argument for parameter 'LiteralPath'. Specify a parameter of type 'Sys
again.
At line:1 char:4
+ ls -l
+ ~~
        + CategoryInfo : InvalidArgument: (:) [Get-ChildItem], ParameterBindingException
        + FullyQualifiedErrorId : MissingArgument,Microsoft.PowerShell.Commands.GetChildItemCommand

I've been happy enough with cmd + mingw/msys. That got me ls, make, and all the same goodies with the same syntax as linux. But if Windows PS is going to have "ls", it should work like "ls" or get out of the way. (Just like they evidently do in linux and macos powershell.)

Comment Re:You may be looking in the wrong place (Score 2) 537

Thanks for your reply. It's an interesting discussion, and indeed, I get a little fed up when even in academia, translational medicine morphs from meaning "translating theory into practice" to meaning "getting patents and making profitable startups." It's needed, but it can sometimes distort the field and culture when it becomes an ends and not a means.

I'm a little curious as to your definition of techie, because a lot of the discussion really boils down to how you define a techie.

I find my techie friends are more informed and intellectually curious than any other group. I'd put them at about equal to my academic friends in this area.

When you say this, this makes me think your Venn diagram for "technies" and "academics" has no intersection. But ask most any grad student, postdoc, or faculty in an engineering, CS, or applied math department (and increasingly many biology departments), and they'll likely regard themselves as techies.

It seems to me a reasonable definition that a techie is a technophile, particularly one who loves, uses, and improves technology in their daily work and hobbies. But if you restrict your label to Silicon Valley and tech startup types, you're lose most of the amateur techies, the open source people, and the citizen scientists.

Again, it's an interesting discussion, so thanks. (And great to meet you here on Slashdot!)

Comment You may be looking in the wrong place (Score 5, Insightful) 537

Most of us who entered science and academia did so to make the world a better place, and many of us are techies. You'd be amazed at home much coding and tech is required for pretty much every area of science today.

We're writing open source software to solve real problems in science and engineering. We're spending the last of our startups on open access for our papers because it's the right thing to do. We're contributing to open data repositories because sharing data makes all our work better. We're writing free content on blogs, code tutorials, and MOOCs for public outreach, because we view our roles as educators seriously.

Most people in academic endure years of low pay and job uncertainty as postdocs and entry-level faculty--and defer or postpone indefinitely having children and buying that starter home--rather than faster and better-paying paths in industry, IP law, and mathematical finance because we do want to make the world a better place, and we're actively working on it.

So, while I agree with your general feeling, take a look around, and you'll see more techies trying make a difference that you might have realized.

Comment Re:Death to publishers (Score 5, Interesting) 172

Well, thats easy to solve:

When we get the right to demand money for whatever we deem is our interlectual property, the next step is to demand that companies like google are not allowed to make their own decisions in regard to what they return as search results. We'll put that under something like "no discrimination" or something.

Sounds like Spain tried to do this almost verbatim:

The Spanish Newspapers Publishersâ(TM) Association (AEDE) is now asking that the Spanish government and EU competition authorities stop Google News from shutting down its operations in the country, âoeto protect the rights of citizens and businesses.â

The media lobby group announced that an end to Spanish Google News would represent âoenot just the closure of another service given its dominant market position,â identifying that the closure would âoeundoubtedly have a negative impact on citizens and Spanish businesses.â

source: [thestack.com]

Comment Re:I believe this violates the Outer Space Treaty (Score 5, Insightful) 256

I am not a legal expert but I believe their plan to produce a nuclear-armed spacecraft violates the Outer Space Treaty (to which Russia is a signatory) and specifically Article IV which says "States Parties to the Treaty undertake not to place in orbit around the earth any objects carrying nuclear weapons or any other kinds of weapons of mass destruction, install such weapons on celestial bodies, or station such weapons in outer space in any other manner." (which sounds like exactly what Russia wants to do)

Then again, with the way the Russian economy is these days, I dont think they have the funds to actually build or launch this thing so it wont matter...

Sounds like it's planned to only ascend when needed, so nothing stationed in space. (And in any event, not in orbit until the point where treaties are moot.)

Comment Re:FP (Score 5, Informative) 152

I read it too, and I fail to see the breakthrough. There are plenty of pseudo random number generators, such as the Mersenne Twister, with very long periods, so just occassionally XORing even a poor quality random number into the feedback loop, is enough to make it completely unpredictable.

Mersenne Twister is pretty much the standard for simulating a uniform distribution in a lot of scientific computing. These depend not only upon unpredictability (useful for avoiding biases, and clearly important in the security realm), but also upon properties of the uniform distribution.

But when we test it out, we find it's still not as great as we'd like: look at a histogram of outputs, and you'll see that until you get really large numbers of function calls, the histogram isn't particularly uniform. (In particular, numbers near the bottom and top of the range don't get called quite as often.) This means that simulation properties that rely upon uniform distributions over both long and short time periods may be thrown off, and short- and mid-time simulation results may well stem from the MT rather than from the mathematical model. Moreover, low-probability events may have artificially smaller probabilities in the simulations (because of the non-uniformity of the distributions near the bottom and top ends of the range).

Over very short numbers of function calls (a few hundred to a few thousand), the outputs can even tend to cluster in a small neighborhood. So suppose that you are simulating a tissue with many cells, and calling MT as your uniform distribution to decide if the cells divide or stay dormant (each with independent probability p, so each cell divides if PRNG/max(PRNG) < p). The math says that for a uniform distribution, you don't need to worry about what order you evaluate your decision across all the cells. But if the PRNG outputs cluster over several sequential calls, then a neighborhood of cells may simultaneously divide if they are all evaluated close to one another sequentially. In analyzing the spatial behavior of such a simulation, you may draw incorrect conclusions in smaller spatial structures that, again, derive from non-uniformity of the PRNG, rather than problems with predictability. (And then you may accept/reject a particular hypothesis or mathematical model pre-maturely.)

So, there's definitely more to it than just unpredictability, depending upon where the code is being used.

Comment Re:Serious question - why not just publish to publ (Score 4, Informative) 191

I'm not in academia, but I've published a bunch of (mostly IT security) research to be freely read by the public under my own copyright or the copyright of a company that's hired me. My serious question is: what is to prevent individual researchers from just publishing what they have as a PDF or WordPress article on a random site on the Internet? (e.g. are there rules in their contract that says they can only publish through so-and-so service, who has the copyright of academic research, etc.)

In part, this is what preprint servers like arxiv and bioarxiv are for.

However, there are deeper-rooted, cultural issues at play here. Academics are rated on their job performance (for keeping your position, finding tenure-track positions, and later attaining tenure) based upon their peer-reviewed publications. Traditionally, this has meant going through the private, paywalled journals.Likewise, getting grants requires publications in peer-reviewed journals, rather than just posting online.

Now, posting in open access journals (like the PLOS family of journals, PeerJ, etc.) helps here, since at the least the access isn't paywalled. But now the academic / lab itself has to pay a much larger publication fee. (Often on the order of $1500 per article.) Moreover, many of said tenure review panels and grant review committees judge you not just on whether you've published, but where. Impact factor matters, and that again tends to steer people towards glammy, paywalled journals like New England Journal of Medicine (which just made a big kerfluffle about research parasites), Nature, Science, etc.)

So, there's a lot going on here. And even the scientists who want to just post preprints and move on are facing tremendous pressures.

Comment Re:8 seconds (Score 3, Informative) 68

How does that actually happen with a smart phone? I mean it's not like you're going to download ISOs to your phone and ...

Mobile hotspot.
For when you don't want to pay the outrageous wifi charges at a hotel conference center, or Starbucks' connection is flaky, or Charter / Comcast / Timewarner crashes for the evening and you have work to do, or ... etc.

Comment Re:Too late (Score 3) 454

A bit unrelated: I was just browsing your website (the one in your signature), and was noting that I couldn't watch the embedded youtube video (talking about this video). They are included as html object element and require flash to be played (which I don't have). Its better to support HTML5 as well by using a more modern embedding code via iframes. It will still offer a fallback for users who can't play back html5 videos, e.g. on outdated browsers. You can get the embed code by clicking "share" and then "embed".

Ah, thanks for the reminder! I worked on embedding those videos back in the HTML4 strict days. (And before YouTube, we had XVID-encoded AVI files, with a support page on how to play the videos. :-/ Embedded video has come a long, long way!)

I completely agree--they should be embedded as real HTML5, particularly as browser support is much more widespread now. And the "share / embed" code works very well for that now. I'll try to get back to it over the weekend.

Thanks for dropping by and giving the work a look! I plan to submit a method paper on PhysiCell (the 3-D agent-based model in the video you linked) and open source it soon. I should have some much cooler videos available for you then. ;-)

Very best -- Paul

Comment Re:Too late (Score 4, Interesting) 454

For what it's worth, we're keeping our NCI-funded cancer/biology projects there for the time being. (We just posted our 3-D diffusion code there in December, and we're about to post 3-D agent-based models and parameter estimation code.) SourceForge was a good and user-friendly home to me when I just got started in open source, so I'm happy to keep trying it now and see where it goes.

We may have some feature requests down the road (some of which may already be there, but hidden behind UI design) ...

Thanks for all your work. -- Paul

Comment Bring back something like freshmeat? (Score 4, Interesting) 1839

I miss the old days where there was a side bar freshmeat feed of new SourceForge releases. Could we possible increase the SlashDot / SourceForge links this way? A running feed of releases would be nice, and it would help bring us back to our FOSS roots.

Also, in the scientific community (I'm in the cancer simulation field), "grand challenges" are popping up, where there would be a dataset or two, and a challenge to create an analysis or modeling tool for those data. Some really amazing creativity can emerge from those challenges.

It would be interesting if such a thing could be done here, similarly to the "ask slashdot" articles, but then linking to a development space on SourceForge to keep it going. I would love to engage the developer community here on our data standards and other cancer projects, and I hope they'd like to pitch in.

Thanks -- Paul

PS: Please consider stopping the SourceForge spam. I'm not sure I need any more "SourceForge Resources" emails on "Flash Storage for Dummies" and business intelligence / analytics / etc.

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