RepeatMasker was developed using TRF version 4.0.4

For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler )

analyses using these ego-level measures can be done using statistical packages like SPSS

UCINET is NetDraw, a visualization tool that has advanced graphic properties.

We’ve designed our products to meet essential needs of journalism through effective online communities.

I don’t want the culture of open source to be organized around a legal definition. I want to zoom out and look at the broader ecosystem (of which the legal definition is one, essential node). A friendlier, more accessible term would make it easier to discuss topics like sustainability, collaboration, and people involved. Those aspects don’t need to be included in the official definition, but they still matter.I still like the term “public software” because it allows more people (including those new to, or unfamiliar with, open source, even if they use or benefit from it) to quickly understand what open source software is and how it should be protected. It doesn’t change the legal definition at all; if anything, it enforces it better, because we would want to define and protect public software exactly as we would any other public resource.

Not every committer has the rights to release or make high level decisions, so we can be much more liberal about giving out commit rights. That increases the committer base for code review and bug triage. As a wider range of expertise in the committer pool smaller changes are reviewed and adjusted without the intervention of the more technical contributors, who can spend their time on reviews only they can do.

The rise of agile coincided with the rise of startups using open source projects. At first, startups just incorporated those projects into their own software. But like any cultural exchange, open source began to affect how startups built products, too.

In short we move all of the new operators to a factory. We group all of the objects of similar lifetime into a single factory

By the way, if the point about being global is that a Singleton can be included in any file and used anywhere in a program, that’s true, but only bad if misused. The Singleton pattern is not inherently bad, it’s misuse is bad

If the singleton class is a “utility class” (e.g. FileUtils, StringUtils, etc.), and has no state, then I would say it’s okay. Such a class is not a liar, per se, because there is no unexpected state change or dependency

ccp.chargePurchaseToCard(100,c); since the logic for purchasing will be in the processor anyway, not the card. Cards don’t process anything

You shouldn’t really be doing this anyway – you should have composed them, possibly via IOC.

It would violate it if you stored a reference to context instead of the engine and later on referred tried to get the engine. For example: class Mechanic { Context context; Mechanic(Context context) { this.context = context; } bool CheckEngine() { return this.context.getEngine().checkIfBusted(); } }

Every time I have to write a test I have to create a graph of objects (the haystack) which no one really needs or cares for, and into this haystack I have to carefully place the needles (the real object of interests) so that the code under test can go and look for them. I have to create the Context just so when I construct the Mechanic it can reach in the Context and get what it realy needs, the Engine. But context is never something which is easy to create. Since context is a kitchen sink which knows just about everything else, its constructor is usually scary. So most of the time I can’t even instantiate Mechanic, not to mention run any tests on it. The testing game is over before it even started

His point seems to be that Constructor Injection can be an anti-pattern if applied too much, particularly if a consumer doesn't need a particular dependency in the majority of cases

The law of leaky abstractions means that whenever somebody comes up with a wizzy new code-generation tool that is supposed to make us all ever-so-efficient, you hear a lot of people saying "learn how to do it manually first, then use the wizzy tool to save time."

A famous example of this is that some SQL servers are dramatically faster if you specify "where a=b and b=c and a=c" than if you only specify "where a=b and b=c" even though the result set is the same. You're not supposed to have to care about the procedure, only the specification. But sometimes the abstraction leaks and causes horrible performance

TCP attempts to provide a complete abstraction of an underlying unreliable network, but sometimes, the network leaks through the abstraction and you feel the things that the abstraction can't quite protect you from. This is but one example of what I've dubbed the Law of Leaky Abstractions

Isolate the dependencies Write the test first Draw the boundary Implement the logic

“the free software movement does this.” And again, I have to say: not quite. 

Convivial tools should be accessible — free, even.

The computer programming the child.”

As such, scrum adopts an empirical approach—accepting that the problem cannot be fully understood or defined, focusing instead on maximizing the team's ability to deliver quickly, to respond to emerging requirements and to adapt to evolving technologies and changes in market conditions.

the study of innovation shows that everything hinges on the hard work of taking a promising idea and making it work — technically, legally, financially, culturally, ecologically. Constraints are great enablers of innovation.

But there’s a downside to the hackathon hype, and our research on designing workplace projects for innovation and learning reveals why. Innovation is usually a lurching journey of discovery and problem solving. Innovation is an iterative, often slow-moving process that requires patience and discipline. Hackathons, with their feverish pace, lack of parameters and winner-take-all culture, discourage this process. We could find few examples of hackathons that have directly led to market success.

what if projects were designed to combine a hacking mindset with rigorous examination of the data and experience they glean? This would reward smart failures that reveal new insights and equip leaders with the information needed to rescale, pivot or axe their projects.

Zoomerang

While the display is appealing and easy to read, it is not customizable

Polldaddy for iOS was a great option for this type of assessment. The layout and design are optimized for the iPad’s screen, and survey results are loaded offline. Be-cause an Internet connection is not required to administer a survey, the researcher has more flexibility in location of survey administration.

Google Forms

unlike Adobe DPS, Inkling, or some other would-be competitors…it’s free.

if the group should decide to fork Moodle together

alliance of Moodle service providers that currently collaborate on Moodle-related projects of mutual interest

Yet there is a growing recognition that provisions must also be made for the data-analysis software that supports the conclusions.

The four freedoms don’t limit us as creators — they open possibilities for us as creators and consumers. When you apply them to software, you get Linux, Webkit/Chrome, and WordPress. When you apply them to medicine, you get the Open Genomics Engine, which is accelerating cancer research and bringing us closer to personalized treatment. When you apply them to companies, you get radically geographically distributed, results-based organizations like Automattic. When you apply them to events you get TEDx, Barcamp, and WordCamp. When you apply them to knowledge, you get Wikipedia.

as of December 2013, 21% of websites are powered by WordPress. One-fifth of the web is built with a tool that anyone can use, change, or improve, whenever and however they want (even more when you count other open source projects

B2 was ultimately abandoned by its creator. If I’d been using it under a proprietary license, that would have been the end — for me, and all its other users. But because we had freedoms 2 and 3, Mike Little and I were able to use the software as a foundation

I’ve spent a third of my life building software based on Stallman’s four freedoms, and I’ve been astonished by the results. WordPress wouldn’t be here if it weren’t for those freedoms, and it couldn’t have evolved the way it has. WordPress was based on a program called B2/cafelog that predated it by two years. I was using B2 because it had freedoms 0 and 1

Without feedback, there are three options: I can believe, without evidence, that I am an awesome programmer.  I can believe, without evidence, that I am a terrible programmer and quit to go do something else.  Or finally, I can believe, without evidence, that I am a terrible programmer somehow successfully pretending to be an awesome programmer.

Familiarity with one another’s communication style also helps them respond to each other quickly, and we know from Csikszentmihalyi’s research that immediate feedback is critical to flow.

It’s free. 

Apache Labs is a place for innovation where committers of the foundation can experiment with new ideas.

all-volunteer

Advice to software development interns

freedom is also a deeply personal thing.

TECHNICAL DEBT: A lot of new code is written very very fast, because that’s what the intersection of the current wave of software development (and the angel investor / venture capital model of funding) in Silicon Valley compels people to do. Funders want companies to scale up, quickly, and become monopolies in their space, if they can, through network effects — a system in which the more people use a platform, the more valuable it is. Software engineers do what they can, as fast as they can. Essentially, there is a lot of equivalent of “duct-tape” in the code, holding things together. If done right, that code will eventually be fixed, commented (explanations written up so the next programmer knows what the heck is up) and ported to systems built for the right scale — before there is a crisis. How often does that get done? I wager that many wait to see if the system comes crashing down, necessitating the fix. By then, you are probably too big to go down for too long, so there’s the temptation for more duct tape. And so on.

I BM GroupTalk

Open Source[edit] LightSide[43] EASE[44] - Published by EdX.

The project will develop an analysis package in the open-source language R and complement it with a step-by-step hands-on manual to make tools available to a broad, international user community that includes academics, scientists working for governments and non-governmental organizations, and professionals directly engaged in conservation practice and land management. The software package will be made publicly available under http://www.clfs.umd.edu/biology/faganlab/movement/.

Three things are required to fully guarantee a repeatable installation using requirements files.

Much as it is not the criminal defense lawyer's place to judge their client regardless of how guilty they are, it is not the doctor's place to force experimental treatment upon a patient regardless of how badly the research is needed, and it is not the priest's place to pass worldly judgement on their flock, it is not the programmer's place to try and decide whether the user is using the software in a "good" way or not.