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# Open source

Short description: Free access to software, information and materials as a concept

Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code,[1] design documents,[2] or content of the product. The open-source model is a decentralized software development model that encourages open collaboration.[3][4] A main principle of open-source software development is peer production, with products such as source code, blueprints, and documentation freely available to the public. The open-source movement in software began as a response to the limitations of proprietary code. The model is used for projects such as in open-source appropriate technology,[5] and open-source drug discovery.[6][7]

Open source promotes universal access via an open-source or free license to a product's design or blueprint, and universal redistribution of that design or blueprint.[8][9] Before the phrase open source became widely adopted, developers and producers have used a variety of other terms. Open source gained hold with the rise of the Internet.[10] The open-source software movement arose to clarify copyright, licensing, domain, and consumer issues.

Generally, open source refers to a computer program in which the source code is available to the general public for use or modification from its original design. Code is released under the terms of a software license. Depending on the license terms, others may then download, modify, and publish their version (fork) back to the community.

Many large formal institutions have sprung up to support the development of the open-source movement, including the Apache Software Foundation, which supports community projects such as the open-source framework Apache Hadoop and the open-source HTTP server Apache HTTP.

## History

Main page: History of free and open-source software

The sharing of technical information predates the Internet and the personal computer considerably. For instance, in the early years of automobile development a group of capital monopolists owned the rights to a 2-cycle gasoline-engine patent originally filed by George B. Selden.[11] By controlling this patent, they were able to monopolize the industry and force car manufacturers to adhere to their demands, or risk a lawsuit.

In 1911, independent automaker Henry Ford won a challenge to the Selden patent. The result was that the Selden patent became virtually worthless and a new association (which would eventually become the Motor Vehicle Manufacturers Association) was formed.[11] The new association instituted a cross-licensing agreement among all US automotive manufacturers: although each company would develop technology and file patents, these patents were shared openly and without the exchange of money among all the manufacturers.[11] By the time the US entered World War II, 92 Ford patents and 515 patents from other companies were being shared among these manufacturers, without any exchange of money (or lawsuits).[11]

Early instances of the free sharing of source code include IBM's source releases of its operating systems and other programs in the 1950s and 1960s, and the SHARE user group that formed to facilitate the exchange of software.[12][13] Beginning in the 1960s, ARPANET researchers used an open "Request for Comments" (RFC) process to encourage feedback in early telecommunication network protocols. This led to the birth of the early Internet in 1969.

The sharing of source code on the Internet began when the Internet was relatively primitive, with software distributed via UUCP, Usenet, IRC, and Gopher. BSD, for example, was first widely distributed by posts to comp.os.linux on the Usenet, which is also where its development was discussed. Linux followed in this model.

### Open source as a term

The term "open source" was first proposed by a group of people in the free software movement who were critical of the political agenda and moral philosophy implied in the term "free software" and sought to reframe the discourse to reflect a more commercially minded position.[14] In addition, the ambiguity of the term "free software" was seen as discouraging business adoption.[15][16] However, the ambiguity of the word "free" exists primarily in English as it can refer to cost. The group included Christine Peterson, Todd Anderson, Larry Augustin, Jon Hall, Sam Ockman, Michael Tiemann and Eric S. Raymond. Peterson suggested "open source" at a meeting[17] held at Palo Alto, California, in reaction to Netscape's announcement in January 1998 of a source code release for Navigator. Linus Torvalds gave his support the following day, and Phil Hughes backed the term in Linux Journal. Richard Stallman, the founder of the free software movement, initially seemed to adopt the term, but later changed his mind.[17][18] Netscape released its source code under the Netscape Public License and later under the Mozilla Public License.[19]

Raymond was especially active in the effort to popularize the new term. He made the first public call to the free software community to adopt it in February 1998.[20] Shortly after, he founded The Open Source Initiative in collaboration with Bruce Perens.[17]

The term gained further visibility through an event organized in April 1998 by technology publisher Tim O'Reilly. Originally titled the "Freeware Summit" and later known as the "Open Source Summit",[21] the event was attended by the leaders of many of the most important free and open-source projects, including Linus Torvalds, Larry Wall, Brian Behlendorf, Eric Allman, Guido van Rossum, Michael Tiemann, Paul Vixie, Jamie Zawinski, and Eric Raymond. At that meeting, alternatives to the term "free software" were discussed. Tiemann argued for "sourceware" as a new term, while Raymond argued for "open source". The assembled developers took a vote, and the winner was announced at a press conference the same evening.[21]

"Open source" has never managed to entirely supersede the older term "free software", giving rise to the combined term free and open-source software (FOSS).

## Economics

Main page: Finance:Open-source economics
Area of application of open source software.[22]
Survey on the reasons for using Open Source in 200 Swiss organizations.[22]

Some economists agree that open-source is an information good[23] or "knowledge good" with original work involving a significant amount of time, money, and effort. The cost of reproducing the work is low enough that additional users may be added at zero or near zero cost – this is referred to as the marginal cost of a product. Copyright creates a monopoly so that the price charged to consumers can be significantly higher than the marginal cost of production. This allows the author to recoup the cost of making the original work. Copyright thus creates access costs for consumers who value the work more than the marginal cost but less than the initial production cost. Access costs also pose problems for authors who wish to create a derivative work—such as a copy of a software program modified to fix a bug or add a feature, or a remix of a song—but are unable or unwilling to pay the copyright holder for the right to do so.

Being organized as effectively a "consumers' cooperative", open source eliminates some of the access costs of consumers and creators of derivative works by reducing the restrictions of copyright. Basic economic theory predicts that lower costs would lead to higher consumption and also more frequent creation of derivative works. Organizations such as Creative Commons host websites where individuals can file for alternative "licenses", or levels of restriction, for their works.[24] These self-made protections free the general society of the costs of policing copyright infringement.

Others argue that since consumers do not pay for their copies, creators are unable to recoup the initial cost of production and thus have little economic incentive to create in the first place. By this argument, consumers would lose out because some of the goods they would otherwise purchase would not be available. In practice, content producers can choose whether to adopt a proprietary license and charge for copies, or an open license. Some goods which require large amounts of professional research and development, such as the pharmaceutical industry (which depends largely on patents, not copyright for intellectual property protection) are almost exclusively proprietary, although increasingly sophisticated technologies are being developed on open-source principles.[25]

There is evidence that open-source development creates enormous value.[26] For example, in the context of open-source hardware design, digital designs are shared for free and anyone with access to digital manufacturing technologies (e.g. RepRap 3D printers) can replicate the product for the cost of materials.[27] The original sharer may receive feedback and potentially improvements on the original design from the peer production community.

Many open source projects have a high economic value. According to the Battery Open Source Software Index (BOSS), the ten economically most important open source projects are:[28][29]

Ranking Project Leading company Market Value
1 Linux Red Hat $16 billion 2 Git GitHub$2 billion
3 MySQL Oracle $1.87 billion 4 Node.js NodeSource ? 5 Docker Docker$1 billion
6 Hadoop Cloudera $3 billion 7 Elasticsearch Elastic$700 million
8 Spark Databricks $513 million 9 MongoDB MongoDB$1.57 billion

### Innovation communities

The principle of sharing pre-dates the open-source movement; for example, the free sharing of information has been institutionalized in the scientific enterprise since at least the 19th century. Open-source principles have always been part of the scientific community. The sociologist Robert K. Merton described the four basic elements of the community—universalism (an international perspective), communalism (sharing information), objectivity (removing one's personal views from the scientific inquiry) and organized skepticism (requirements of proof and review) that describe the (idealised) scientific community.

These principles are, in part, complemented by US law's focus on protecting expression and method but not the ideas themselves. There is also a tradition of publishing research results to the scientific community instead of keeping all such knowledge proprietary. One of the recent initiatives in scientific publishing has been open access—the idea that research should be published in such a way that it is free and available to the public. There are currently many open access journals where the information is available free online, however most journals do charge a fee (either to users or libraries for access). The Budapest Open Access Initiative is an international effort with the goal of making all research articles available free on the Internet.

The National Institutes of Health has recently proposed a policy on "Enhanced Public Access to NIH Research Information". This policy would provide a free, searchable resource of NIH-funded results to the public and with other international repositories six months after its initial publication. The NIH's move is an important one because there is significant amount of public funding in scientific research. Many of the questions have yet to be answered—the balancing of profit vs. public access, and ensuring that desirable standards and incentives do not diminish with a shift to open access.

Benjamin Franklin was an early contributor eventually donating all his inventions including the Franklin stove, bifocals, and the lightning rod to the public domain.

New NGO communities are starting to use the open-source technology as a tool. One example is the Open Source Youth Network started in 2007 in Lisboa by ISCA members.[96]

Open innovation is also a new emerging concept which advocate putting R&D in a common pool. The Eclipse platform is openly presenting itself as an Open innovation network.[97]

### Arts and recreation

Copyright protection is used in the performing arts and even in athletic activities. Some groups have attempted to remove copyright from such practices.[98]

In 2012, Russian music composer, scientist and Russian Pirate Party member Victor Argonov presented detailed raw files of his electronic opera "2032"[99] under free license CC-BY-NC 3.0 (later relicensed under CC-BY-SA 4.0[100]). This opera was originally composed and published in 2007 by Russian label MC Entertainment as a commercial product, but then the author changed its status to free. In his blog[101] he said that he decided to open raw files (including wav, midi and other used formats) to the public in order to support worldwide pirate actions against SOPA and PIPA. Several Internet resources[102][103][104][105] called "2032" the first open-source musical opera in history.

### Other related movements

The following are events and applications that have been developed via the open source community, and echo the ideologies of the open source movement.[106]

Open Education Consortium — an organization composed of various colleges that support open source and share some of their material online. This organization, headed by Massachusetts Institute of Technology, was established to aid in the exchange of open source educational materials.

Wikipedia — user-generated online encyclopedia with sister projects in academic areas, such as Wikiversity — a community dedicated to the creation and exchange of learning materials[107]

Project Gutenberg — prior to the existence of Google Scholar Beta, this was the first supplier of electronic books and the very first free library project[107]

Synthetic Biology- This new technology is potentially important because it promises to enable cheap, lifesaving new drugs as well as helping to yield biofuels that may help to solve our energy problem. Although synthetic biology has not yet come out of its "lab" stage, it has potential to become industrialized in the near future. In order to industrialize open source science, there are some scientists who are trying to build their own brand of it.[108]

### Ideologically-related movements

The open-access movement is a movement that is similar in ideology to the open source movement. Members of this movement maintain that academic material should be readily available to provide help with "future research, assist in teaching and aid in academic purposes." The Open access movement aims to eliminate subscription fees and licensing restrictions of academic materials[109]

The free-culture movement is a movement that seeks to achieve a culture that engages in collective freedom via freedom of expression, free public access to knowledge and information, full demonstration of creativity and innovation in various arenas and promotion of citizen liberties.[110]

Creative Commons is an organization that "develops, supports, and stewards legal and technical infrastructure that maximizes digital creativity, sharing, and innovation." It encourages the use of protected properties online for research, education, and creative purposes in pursuit of a universal access. Creative Commons provides an infrastructure through a set of copyright licenses and tools that creates a better balance within the realm of "all rights reserved" properties.[111] The Creative Commons license offers a slightly more lenient alternative to "all rights reserved" copyrights for those who do not wish to exclude the use of their material.[112]

The Zeitgeist Movement is an international social movement that advocates a transition into a sustainable "resource-based economy" based on collaboration in which monetary incentives are replaced by commons-based ones with everyone having access to everything (from code to products) as in "open source everything".[113][114] While its activism and events are typically focused on media and education, TZM is a major supporter of open source projects worldwide since they allow for uninhibited advancement of science and technology, independent of constraints posed by institutions of patenting and capitalist investment.[115]

P2P Foundation is an "international organization focused on studying, researching, documenting and promoting peer to peer practices in a very broad sense". Its objectives incorporate those of the open source movement, whose principles are integrated in a larger socio-economic model.[116]

## References

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24. Wittbrodt, B.T.; Glover, A.G.; Laureto, J.; Anzalone, G.C.; Oppliger, D.; Irwin, J.L.; Pearce, J.M. (2013). "Life-cycle economic analysis of distributed manufacturing with open-source 3-D printers". Mechatronics 23 (6): 713–726. doi:10.1016/j.mechatronics.2013.06.002.
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33. Faraj, S., Jarvenpaa, S. L., & Majchrzak, Ann (2011). Knowledge Collaboration in Online Communities. Organization Science, 22(5), 1224-1239, doi:10.1287/orsc.1100.0614
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42. "FAQ | LucidWorks". Lucidimagination.com. 2012-08-08.
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44. "Arduino — HomePage". Arduino.cc.
46. Arkinstall, Kam (2 December 2013). "Mega Bites – how open data and gastronomy are proving a recipe for success". Research In Progress Blog. biomedcentral.com.
47. The concept expands upon a statement found in the Free Software Definition: "Free software is a matter of liberty, not price. To understand the concept, you should think of 'free' as in 'free speech' not as in 'free beer.'"
48. Stallman, Richard M.. "The Gnu Organisation: What is free software?". Gnu.org.
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53. "Finding cures for tropical diseases: is open source an answer?". PLOS Med. 1 (3): e56. December 2004. doi:10.1371/journal.pmed.0010056. PMID 15630466.
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## A Bundle Method for Integrated Multi-Depot Vehicle and Duty Scheduling in Public Transit

Please always quote using this URN: urn:nbn:de:0297-zib-7898
• This article proposes a Lagrangean relaxation approach to solve integrated duty and vehicle scheduling problems arising in public transport. The approach is based on the proximal bundle method for the solution of concave decomposable functions, which is adapted for the approximate evaluation of the vehicle and duty scheduling components. The primal and dual information generated by the bundle method is used to guide a branch-and-bound type algorithm. Computational results for large-scale real-world integrated vehicle and duty scheduling problems with up to 1,500 timetabled trips are reported. Compared with the results of a classical sequential approach and with reference solutions, integrated scheduling offers remarkable potentials in savings and drivers' satisfaction.

$Rev: 13581$

format: plain


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# Solver to Analyze and Graph a Linear Function

 Step by step worksheet solver, to analyze the slope and intercept of a linear function and graph it, is presented. Unlimited number of questions may be generated including their detailed solutions and expalnations. The graph of the linear function is located at the bottom of the page. Step by step solution STEP 1: Use the fact that for linear functions written in the form $f(x)=mx+b$, $m$ is the rate of change (or slope) and $b$ is the $y$-intercept to write the rate of change and $y$-intrcept of the given function. STEP 2: Use the sign of rate of change (or slope) to determine whether the given function is an increasing or a decreasing one. STEP 3: Use a graph to check that $rise = slope \times run$. Graphical Meaning of Solution Below are shown the graph of the given function ¤f¤ (green) and the rise ¤\Delta y¤ and the run ¤\Delta x¤ (red). (Change scales if necessary)
More Step by Step Math Worksheets Solvers New !


text:
# In the given figure, O is the center of the circle. OA = 3 cm, AC = 3 cm and OM ⊥ AC. What is ∠ABC equal to?

730 views
in Circles
closed

In the given figure, O is the center of the circle. OA = 3 cm, AC = 3 cm and OM ⊥ AC. What is ∠ABC equal to?

(a) 60°

(b) 45°

(c) 30°

(d) None of these

+1 vote
by (24.6k points)
selected by

Given OA = 3 cm ⇒ OC = 3 cm (radii of the circle)

Also AC = 3 cm ⇒ OA = OC = AC ⇒ ∆ AOC is equilateral

⇒ ∠AOC = 60°.

⇒ ∠ABC = $\frac{1}{2}$ $\times$ ∠AOC

= 30° (Angle subtended by an arc of a circle at the center is double the angle subtended by it at any point on the remaining part of the circle.)


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# What does this Java error mean? Why is it raised?

I want to launch some kernels on a cluster that uses SGE. The server's operating system is Linux Cent-OS. According to Mathematica documentation, I've added these commands inside my code:

Needs["CLusterIntegration"]
kernels=LaunchKernels[SGE["mnt-cluster.org"],8]

DistributeDefinitions[F]; (*F is defined in previous lines, and itself cannot be parallelized efficiently.*)
Parallelize[TST = Map[F, {a1, a2, a3, a4}]]; (*An example of what I want to be done on parallel nodes.*)

CloseKernels[kernels]

but once I ran it, these errors were raised:

Java::excptn: A Java exception occurred: java.lang.UnsatisfiedLinkError: no drmaa in java.library.path
at com.sun.grid.drmaa.SessionImpl\$1.run(SessionImpl.java:58)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.grid.drmaa.SessionImpl.<clinit>(SessionImpl.java:56)
at com.sun.grid.drmaa.SessionFactoryImpl.getSession(SessionFactoryImpl.java:59).
SGE::load: Cannot find components required for SGE. >>

and another time I ran it again the list of error has changed to only this one:

Java::excptn: A Java exception occurred: java.lang.NoClassDefFoundError: Could not initialize class com.sun.grid.drmaa.SessionImpl
at com.sun.grid.drmaa.SessionFactoryImpl.getSession(SessionFactoryImpl.java:59).
SGE::load: Cannot find components required for SGE. >>

I can find the file "drmaa" on the server on which I've installed Mathematica8.
I'd appreciate anyone who may help me to find out why these errors raised and how should I resolve them.

• A shared library that should be on the path is missing or the path is incorrect. Is the location you found drmaa (is that drmma.so?) in your path (not classpath)? – Ymareth Dec 9 '14 at 17:47
• @Ymareth That time I faced the problem, according to this MathGroup archive, I updated my CLASSPATH to where I found drmaa.jar, which was compeletly different with the addresses in the above link. But I didn't found the others: jgdi and juti. – Toughee Dec 18 '14 at 4:22
• @Ymareth I also can find drmaa.so and drmaa.so.1.0 inside a folder besides drmaa.jar` not exactly in the path. – Toughee Dec 18 '14 at 4:25
• What are your values for the PATH and LD_LIBRARY_PATH environment variables? This is to do with loading native shared libraries it is (I believe) nothing to do with CLASSPATH. – Ymareth Dec 18 '14 at 9:52


text:
# Cannot Remove or Edit Properties of an Attachment with Umlaut Characters

#### Still need help?

The Atlassian Community is here for you.

## Symptoms

1. Attachment contains an umlaut or other special character, e.g. äüö.xls

2. Attachment deletion fails with "Not Permitted" page even though user has sufficient permission:

Not Permitted
You are not permitted to perform this operation.
3. Viewing or editing the properties of the attachment leads to a System Error page with the following stacktrace:

java.lang.NullPointerException
at com.atlassian.confluence.pages.actions.MoveAttachmentAction.bootstrap(MoveAttachmentAction.java:112)

## Cause

• The application server URL encoding is not set to UTF-8.
• The URL encoding attribute is written wrongly or is incorrectly cased, hence Tomcat doesn't understand and pick it up. For example: URIencoding is wrong because it should have an uppercase E, and URlEncoding is wrong because it has a lowercase L instead of an uppercase I. The correct attribute is URIEncoding. It should look like this:

URIEncoding="UTF-8"

## Resolution

1. Set your application server URL encoding to UTF-8 as described here. For example, in Tomcat add URIEncoding="UTF-8" to the HTTP connector.
2. Restart Confluence.

You might need to apply this to all available connectors, too (e.g. AJP connector).


text:
shade_confidence_interval() plots a confidence interval region on top of visualize() output. The output is a ggplot2 layer that can be added with +. The function has a shorter alias, shade_ci().

Learn more in vignette("infer").

shade_confidence_interval(
endpoints,
color = "mediumaquamarine",
fill = "turquoise",
...
)

shade_ci(endpoints, color = "mediumaquamarine", fill = "turquoise", ...)

## Arguments

endpoints The lower and upper bounds of the interval to be plotted. Likely, this will be the output of get_confidence_interval(). For calculate()-based workflows, this will be a 2-element vector or a 1 x 2 data frame containing the lower and upper values to be plotted. For fit()-based workflows, a (p + 1) x 3 data frame with columns term, lower_ci, and upper_ci, giving the upper and lower bounds for each regression term. For use in visualizations of assume() output, this must be the output of get_confidence_interval(). A character or hex string specifying the color of the end points as a vertical lines on the plot. A character or hex string specifying the color to shade the confidence interval. If NULL then no shading is actually done. Other arguments passed along to \ggplot2\ functions.

## Value

If added to an existing infer visualization, a \ggplot2\ object displaying the supplied intervals on top of its corresponding distribution. Otherwise, an infer_layer list.

Other visualization functions: shade_p_value()

## Examples

# find the point estimate---mean number of hours worked per week
point_estimate <- gss %>%
specify(response = hours) %>%
calculate(stat = "mean")

# ...and a bootstrap distribution
boot_dist <- gss %>%
# ...we're interested in the number of hours worked per week
specify(response = hours) %>%
# generating data points
generate(reps = 1000, type = "bootstrap") %>%
# finding the distribution from the generated data
calculate(stat = "mean")

# find a confidence interval around the point estimate
ci <- boot_dist %>%
get_confidence_interval(point_estimate = point_estimate,
# at the 95% confidence level
level = .95,
# using the standard error method
type = "se")

# and plot it!
boot_dist %>%
visualize() +

# or just plot the bounds
boot_dist %>%
visualize() +

# you can shade confidence intervals on top of
# theoretical distributions, too---the theoretical
# distribution will be recentered and rescaled to
# align with the confidence interval
sampling_dist <- gss %>%
specify(response = hours) %>%
assume(distribution = "t")

visualize(sampling_dist) +

# \donttest{
# to visualize distributions of coefficients for multiple
# explanatory variables, use a fit()-based workflow

# fit 1000 linear models with the hours variable permuted
null_fits <- gss %>%
specify(hours ~ age + college) %>%
hypothesize(null = "independence") %>%
generate(reps = 1000, type = "permute") %>%
fit()

null_fits
#> # A tibble: 3,000 × 3
#> # Groups:   replicate [1,000]
#>    replicate term          estimate
#>        <int> <chr>            <dbl>
#>  1         1 intercept     42.1
#>  2         1 age           -0.0141
#>  3         1 collegedegree -0.414
#>  4         2 intercept     37.8
#>  5         2 age            0.0809
#>  6         2 collegedegree  0.881
#>  7         3 intercept     41.8
#>  8         3 age            0.00730
#>  9         3 collegedegree -2.07
#> 10         4 intercept     41.6
#> # … with 2,990 more rows

# fit a linear model to the observed data
obs_fit <- gss %>%
specify(hours ~ age + college) %>%
fit()

obs_fit
#> # A tibble: 3 × 2
#>   term          estimate
#>   <chr>            <dbl>
#> 1 intercept     40.6
#> 2 age            0.00596
#> 3 collegedegree  1.53

# get confidence intervals for each term
conf_ints <-
get_confidence_interval(
null_fits,
point_estimate = obs_fit,
level = .95
)

# visualize distributions of coefficients
# generated under the null
visualize(null_fits)


text:
# Problem with Shelah and Stern's paper on the Hanf number of the theory of Banach spaces

I have been trying to understand "The Hanf number of the first order theory of Banach spaces" by Shelah and Stern (Trans. AMS 244 (1978) 147-241). They construct a normed space $M$ from a Hilbert space $\cal H$ by taking the unit ball of $M$ to be the intersection of that of $\cal H$ with the halfspaces defined by $(x, \pm a) \le 1 - \delta_a$ for certain unit vectors $a$ and small $\delta_a >0$. They then need to show that the $\cal H$-unit ball is definable in $M$ using a first order language with symbols for vector addition and membership of the $M$-unit ball. With this in view, in their Lemma 2.9, they claim certain of the vectors $a$ are definable, but they don't have what they need to apply the lemma they appeal to for this (they have an inequality $\|b\| \le (1 - \delta)^{-1}$ but their Lemma 2.3 needs the opposite inequality).

So this looks like a bug. I suspect it can be fixed, e.g., by taking the unit ball to be the convex hull of the proposed one and the vectors $\pm a$. But this would be quite disruptive to the rest of the argument, I suspect.

My questions are (1) have I missed something so that Shelah and Stern's proof does actually go through more or less as its stands, or (2) is there another reference that gives a correct proof of these results.

-


text:
# 7.01: Types of Chemical Reactions - Double Displacement Reactions

Learning Objectives

• Recognize chemical reactions as double-replacement reactions.
• Use the periodic table and solubility rules to predict whether double-replacement reactions will occur.

Up to now, we have presented chemical reactions as a topic, but we have not discussed how the products of a chemical reaction can be predicted. Here we will begin our study of certain types of chemical reactions that allow us to predict what the products of the reaction will be.

A double-replacement reaction occurs when parts of two ionic compounds are exchanged, making two new compounds. A characteristic of a double-replacement equation is that there are two compounds as reactants and two different compounds as products. An example is

$\ce{CuCl2(aq) + 2AgNO3(aq) → Cu(NO3)2(aq) + 2AgCl(s)}$

There are two equivalent ways of considering a double-replacement equation: either the cations are swapped, or the anions are swapped. (You cannot swap both; you would end up with the same substances you started with.) Either perspective should allow you to predict the proper products, as long as you pair a cation with an anion and not a cation with a cation or an anion with an anion.

Example $$\PageIndex{1}$$

What cations and anions are participating in this chemical reaction?

$\ce{BaCl2 + Na2SO4 → }$

Solution

Looking at a periodic table we can determine the charges for the barium ion, the chloride ion and the sodium ion:

Ba2+ (barium is in group 2A)

Na+ (sodium is in group 1A)

Cl- (chloride is in group 7A)

Our final anion is a polyatomic ion, so we can't use the periodic table if we don't have the charge on sulfate memorized, but we can use the charge on sodium to figure it out.

We need two Na+ to cancel out the charge on our SO4 so the charge on our sulfate has to be 2-:

2(+1) + x = 0 --> x = -2

All together we have Ba2+, Cl-, Na+ and SO42- participating in our reaction.

Example $$\PageIndex{2}$$

Predict the products of this double-replacement equation:

$\ce{BaCl2 + Na2SO4 → }$

Solution

We saw in example $$\PageIndex{1}$$ that the ions participating in the reaction were Ba2+, Cl-, Na+ and SO42-.  We know that like charges repel each other, so our anions (Ba2+ and Na+) are not going to come together, same thing goes for our cations (Cl- and SO42-). For a chemical reaction to have taken place something has to have changed so we can't put the barium back with the chloride and the sodium back with the sulfate. This leaves pairing the barium ion with our sulfate and the sodium ion with our chloride as our only option.

$\ce{Ba^2+ + SO4^2- → BaSO4}$

$\ce{Na+ + Cl- → NaCl}$

Putting this all together and balancing our chemical equation we get

$\ce{BaCl2 + Na2SO4 → BaSO4 + 2 NaCl}$

Exercise $$\PageIndex{3}$$

Predict the products of this double-replacement equation:

$\ce{KBr + AgNO3 → }$

KNO3 and AgBr

Predicting whether a double-replacement reaction occurs is somewhat more difficult than predicting a single-replacement reaction. However, there is one type of double-replacement reaction that we can predict: the precipitation reaction. A precipitation reaction occurs when two ionic compounds are dissolved in water and form a new ionic compound that does not dissolve; this new compound falls out of solution as a solid precipitate. The formation of a solid precipitate is the driving force that makes the reaction proceed.

Figure $$\PageIndex{1}$$: Illustration of the double-replacement reaction between aqueous silver fluoride (AgF) and aqueous potassium chloride (KCl).

As illustrated in Figure $$PageIndex{1}$$ upon mixing the AgF solution and the KCl solution the silver ion (Ag+) and the chloride ion (Cl-) combine to form a insoluble salt, the precipitate. As the salt is insoluble it will not dissolve in water and we use the (s) symbol for solid.  If no precipitate formed we would essentially have given the silver, fluoride, potassium and chloride ions a change of scenery, but they would still be floating around as ions. In this case no reaction occurs.

Figure $$\PageIndex{1}$$: The formation of a silver chloride precipitate. The precipitate is the white solid we see appearing in the solution
By Luisbrudna - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/inde...curid=40139259

To judge whether double-replacement reactions will occur, we need to know what kinds of ionic compounds form precipitates. For this, we use solubility rules, which are general statements that predict which ionic compounds dissolve (are soluble) and which do not (are not soluble or insoluble). Table 4.3.1 - Some Useful Solubility Rules, lists some general solubility rules. We need to consider each ionic compound (both the reactants and the possible products) in light of the solubility rules. If a compound is soluble, we use the (aq) label with it, indicating it dissolves. If a compound is not soluble, we use the (s) label with it and assume that it will precipitate out of solution. If everything is soluble, then no reaction will be expected.

 These compounds generally dissolve in water (are soluble): Exceptions: All compounds of Li+, Na+, K+, Rb+, Cs+, and NH4+ None All compounds of NO3− and C2H3O2− None Compounds of Cl−, Br−, I− Ag+, Hg22+, Pb2+ Compounds of SO42- Hg22+, Pb2+, Sr2+, Ba2+ These compounds generally do not dissolve in water (are insoluble): Exceptions: Compounds of CO32− and PO43− Compounds of Li+, Na+, K+, Rb+, Cs+, and NH4+ Compounds of OH− Compounds of Li+, Na+, K+, Rb+, Cs+, NH4+, Sr2+, and Ba2+

For example, consider the possible double-replacement reaction between Na2SO4 and SrCl2. The solubility rules say that all ionic sodium compounds are soluble and all ionic chloride compounds are soluble except for Ag+, Hg22+, and Pb2+, which are not being considered here. Therefore, Na2SO4 and SrCl2 are both soluble. The possible double-replacement reaction products are NaCl and SrSO4. Are these soluble? NaCl is (by the same rule we just quoted), but what about SrSO4? Compounds of the sulfate ion are generally soluble, but Sr2+ is an exception: we expect it to be insoluble-a precipitate. Therefore, we expect a reaction to occur, and the balanced chemical equation would be

$\ce{Na2SO4(aq) + SrCl2(aq) → 2NaCl(aq) + SrSO4(s)}$

You would expect to see a visual change corresponding to SrSO4 precipitating out of solution (Figure $$\PageIndex{2}$$).

Example $$\PageIndex{4}$$:

Will a double-replacement reaction occur? If so, identify the products.

1. Ca(NO3)2 + KBr → ?
2. NaOH + FeCl2 → ?

Solution

1. According to the solubility rules, both Ca(NO3)2 and KBr are soluble. Now we consider what the double-replacement products would be by switching the cations (or the anions)-namely, CaBr2 and KNO3. However, the solubility rules predict that these two substances would also be soluble, so no precipitate would form. Thus, we predict no reaction in this case.
2. According to the solubility rules, both NaOH and FeCl2 are expected to be soluble. If we assume that a double-replacement reaction may occur, we need to consider the possible products, which would be NaCl and Fe(OH)2. NaCl is soluble, but, according to the solubility rules, Fe(OH)2 is not. Therefore, a reaction would occur, and Fe(OH)2(s) would precipitate out of solution. The balanced chemical equation is $\ce{2NaOH(aq) + FeCl2(aq) → 2NaCl(aq) + Fe(OH)2(s)}$

Exercise $$\PageIndex{4}$$

$\ce{Sr(NO3)2 + KCl → }$


text:
# Why does the negative sign arise in this thermodynamic relation?

This is not a simple application of partial derivatives, since the variables that are being held constant vary here, but an instance of the triple product rule, which says that for any three quantities $$x,y,z$$ depending on each other, the relation $$\left(\frac{\partial x}{\partial y}\right)_z\left(\frac{\partial y}{\partial z} \right)_x\left(\frac{\partial z}{\partial x}\right)_y = -1$$ holds.

This all starts from the basic relationship $$dP=\left(\frac{\partial P}{\partial T}\right)_VdT+\left(\frac{\partial P}{\partial V}\right)_TdV$$Since, at constant pressure, dP=0, if we solve for dT/dV at constant pressure, we obtain: $$\left(\frac{\partial T}{\partial V}\right)_P=-\frac{\left(\frac{\partial P}{\partial V}\right)_T}{\left(\frac{\partial P}{\partial T}\right)_V}$$

Other answers have given the mathematical reasons, but as these are physical functions it’s always nice to relate back to physical intuition.

Thinking of an ordinary substance – a lump of “stuff”, doesn’t matter whether it’s a solid or a gas or whatever – if you decrease the volume available to it, the pressure should go up. In fact that is exactly how we physically put a sample under pressure. So the left-hand side should be negative.

On the other hand, if you increase the temperature (usually) the pressure should increase at constant volume, or alternatively the volume should increase at constant pressure.1 So both of the factors on the right-hand side should be positive.2

So we had better include a minus sign, to at least get the signs to match on both sides of the equation.

1. If you’re thinking about a material with negative thermal expansion, then both of these factors should instead be negative, but again the right-hand side of the equation ends up positive.
2. To be precise, I have used another identity here: that $$(\partial T/\partial V)_P = (\partial V/\partial T)_P^{-1}$$.


text:
Error: Bad BCF record - shared section malformed or too short after vcftools filtering
0
0
Entering edit mode
18 months ago
yvanpapa • 0

Hi everyone,

I am trying to use vcftools (0.1.16) to filter a vcf file using the following command:

F1="--max-missing 0.5 --mac 3 --minQ 30 --remove-indels"

vcftools --vcf variants_input.vcf --out variants_output.F1 \$F1 --recode-INFO-all --recode-bcf

With that, I get my output "variants_output.F1.recode.bcf" and this report:

Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
After filtering, kept 27 out of 27 Individuals
Outputting BCF file...
After filtering, kept 10473667 out of a possible 598905538 Sites
Run Time = 6576.00 seconds

It seems to me the warnings are not important, and the filtering actually worked given the report. However, when I try to use bcf stats (bcftools 1.9) on my new output, I get a message telling me that the BCF is corrupted or something and that it cannot be stated

bcftools    stats variants_output.F1.recode.bcf > variants_output.F1.recode.bcf.stats.txt
[E::bcf_record_check] Bad BCF record - shared section malformed or too short

Is this caused by the warnings, or something else? I also read somewhere else on the forum that vcftools should not be used anymore but without giving a reason... is it deprecated?

Any help would be greatly appreciated.

vcf bcf filtering SNP • 723 views
2
Entering edit mode

Hello yvanpapa ,

there is no active development in vcftools so I would call it deprecated. Use bcftoolsinstead.

Could you please show the header and the first few variants of your vcf file before you filter? bcftools is very strict about the vcf specification. So we have to make sure you have a valid vcf file.

fin swimmer

0
Entering edit mode

Hi finswimmer,

Thanks a lot for the fast answer.

According to https://github.com/vcftools/vcftools/issues/134 the warning is "just a warning that vcftools doesn't know how to handle the comma within the Description tag. If you remove that comma in the description, the warning will go away. Otherwise, it can generally be ignored." Although I don't find it practical in a routine pipeline to remove manually those comas every time.

I doubt the vcf is not valid because I had no problems using bcftools stats on vcf and bcf files before using vcftools.

I guess I will perform the filtering with bcftools instead. I am pretty new to this but it seems to me it provides the same filtering tools anyway?

1
Entering edit mode

just a warning that vcftools doesn't know how to handle the comma within the Description tag.

What? It is absolutely usual that there are commas in the description tag. If vcftools cannot handle it, that's a bug.

You can use bcftools for filtering nearly everything. Have a look at the several options in bcftools view.

fin swimmer


text:
# Hot chocolate effect

The hot chocolate effect, also known as the allassonic effect, is a phenomenon of wave mechanics first documented in 1982 by Frank Crawford, where the pitch heard from tapping a cup of hot liquid rises after the addition of a soluble powder.[1][2] It was first observed in the making of hot chocolate or instant coffee, but also occurs in other situations such as adding salt to supersaturated hot water or cold beer. Recent research has found many more substances which create the effect, even in initially non-supersaturated liquids.[3]

It can be observed by pouring hot milk into a mug, stirring in chocolate powder, and tapping the bottom of the mug with a spoon while the milk is still in motion. The pitch of the taps will increase progressively with no relation to the speed or force of tapping. Subsequent stirring of the same solution (without adding more chocolate powder) will gradually decrease the pitch again, followed by another increase. This process can be repeated a number of times, until equilibrium has been reached.[4] Upon initial stirring, entrained gas bubbles reduce the speed of sound in the liquid, lowering the frequency. As the bubbles clear, sound travels faster in the liquid and the frequency increases.

## Origin of the phenomenon

The phenomenon is explained by the effect of bubble density on the speed of sound in the liquid. The note heard is the frequency of a standing wave where a quarter wavelength is the distance between the base of the mug and the liquid surface. This frequency f is equal to the speed v of the wave divided by four times the height of the water column h:

${\displaystyle f={\frac {1}{4}}{\frac {v}{h}}}$

The speed of sound v in a homogeneous liquid or gas is dependent on the fluid's mass density (${\displaystyle \rho }$) and Adiabatic Bulk modulus (${\displaystyle K}$), according to the Newton-Laplace formula:

${\displaystyle v={\sqrt {\frac {K}{\rho }}}}$

Water is approximately 800 times denser than air, and air is approximately 15,000 times more compressible than water. When water is filled with air bubbles, however, the fluid's density is very close to the density of water, but the compressibility will be the compressibility of air. This greatly reduces the speed of sound in the liquid. Wavelength is constant for a given volume of fluid, therefore the frequency (pitch) of the sound will decrease as long as gas bubbles are present.[1]

Different rates of bubble formation will generate different acoustic profiles, allowing differentiation of the added solutes.[3][5][6]


text:
### Home > PC3 > Chapter 8 > Lesson 8.3.4 > Problem8-138

8-138.
1. Rewrite each expression as the sine, cosine, or tangent of an angle. Homework Help ✎

Look at the angle difference formula for sine.

Look at the angle sum formula for cosine.

Look at the angle difference formula for tangent.