Monthly Archives: August 2014

Scrivener on Linux: Oh Well…

UPDATE (January 2, 2016): The makers of Scrivener have decided to abandon their Linux project. Kudos for them for giving it a try. The Scrivener on Linux users were not many, and almost nobody donated to the project, and as far as I can tell, the project was not OpenSource and thus could not have attracted much of an interest among a community of mostly OpenSourceHeads.

So, I’m no longer recommending that you mess around with Scrivener on Linux, as it is no longer maintained. Back to emacs, everybody!

Scrivener is a program used by authors to write and manage complex documents, with numerous parts, chapters, and scenes. It allows the text to be easily reorganized, and it has numerous ways in which the smallest portion of the text, the “scene,” and larger collections of text can be associated with notes and various kinds of meta-data. It is mainly a Mac program but a somewhat stripped down beta version is available for Linux.

In some ways, Scrivener is the very embodiment of anti-Linux, philosophically. In Linux, one strings together well developed and intensely tested tools on data streams to produce a result. So, to author a complex project, create files and edit them in a simple text editor, using some markdown. Keep the files organized in the file system and use file names carefully chosen to keep them in order in their respective directories. when it comes time to make project-wide modifications, use grep and sed to process all of the files at once or selected files. Eventually, run the files through LaTeX to produce beautiful output. Then, put the final product in a directory where people can find it on Gopher.

Gopher? Anyway …

On the other hand, emacs is the ultimate linux program. Emacs is a text editor that is so powerful and has so many community-contributed “modes” (like add-ins) that it can be used as a word processor, an email client, a calendar, a PIM, a web browser, an operating system, to make coffee, or to stop that table with the short leg from rocking back and forth. So, in this sense, a piece of software that does everything is also linux, philosophically.

And so, Scrivener, despite what I said above, is in a way the very embodiment of Linux, philosophically.

I’ve been using Scrivener on a Mac for some time now, and a while back I tried it on Linux. Scrivener for the Mac is a commercial product you must pay money for, though it is not expensive, but the Linux version, being highly experimental and probably unsafe, is free. But then again, this is Linux. We eat unsafe experimental free software for breakfast. So much that we usually skip lunch. Because we’re still fixing breakfast. As it were.

When you create a Scrivener project, you can chose among a number of templates.  The Scrivener community has created a modest number of alternatives, and you can create your own. The templates produce binders with specific helpful layouts.
When you create a Scrivener project, you can chose among a number of templates. The Scrivener community has created a modest number of alternatives, and you can create your own. The templates produce binders with specific helpful layouts.

Anyway, here’s what Scrivener does. It does everything. The full blown Mac version has more features than the Linux version, but both are feature rich. To me, the most important things are:

A document is organised in “scenes” which can be willy nilly moved around in relation to each other in a linear or hierarchical system. The documents are recursive, so a document can hold other documents, and the default is to have only the text in the lower level document as part of the final product (though this is entirely optional). A document can be defined as a “folder” which is really just a document that has a file folder icon representing it to make you feel like it is a folder.

The main scrivener work area with text editor (center), binder and inspector.
The main scrivener work area with text editor (center), binder and inspector.
Associated with the project, and with each separate document, is a note taking area. So, you can jot notes project-wide as you work, like “Don’t forget to write the chapter where everyone dies at the end,” or you can write notes on a given document like “Is this where I should use the joke about the slushy in the bathroom at Target?”

Each scene also has a number of attributes such as a “label” and a “status” and keywords. I think keywords may not be implemented in the Linux version yet.

Typically a project has one major folder that has all the actual writing distributed among scenes in it, and one or more additional folders in which you put stuff that is not in the product you are working on, but could be, or was but you pulled it out, or that includes research material.

You can work on one scene at a time.  Scenes have meta-data and document notes.
You can work on one scene at a time. Scenes have meta-data and document notes.
The scenes, folders, and everything are all held together with a binder typically displayed on the left side of the Scrivener application window, showing the hierarchy. A number of templates come with the program to create pre-organized binder paradigms, or you can just create one from scratch. You can change the icons on the folders/scenes to remind you of what they are. When a scene is active in the central editing window, you can display an “inspector” on the right side, showing the card (I’ll get to that later) on top the meta data, and the document or project notes. In the Mac version you can create additional meta-data categories.

Scrivenings Mode
Scrivenings Mode
An individual scene can be displayed in the editing window. Or, scenes can be shown as a collection of scenes in what is known as “Scrivenings mode.” Scrivenings mode is more or less standard word processing mode where all the text is simply there to scroll through, though scene titles may or may not be shown (optional).

A lot of people love the corkboard option. I remember when PZ Myers discovered Scrivener he raved about it. The corkboard is a corkboard (as you may have guessed) with 3 x 5 inch virtual index cards, one per scene, that you can move around and organize as though that was going to help you get your thoughts together. The corkboard has the scene title and some notes on what the scene is, which is yet another form of meta-data. I like the corkboard mode, but really, I don’t think it is the most useful features. Come for the corkboard, stay for the binder and the document and project notes!

Corkboard Mode
Corkboard Mode
When you are ready to do something outside of scrivener with your project, you compile it. You can compile it into an ebook, a file compatible with most word processors, a PDF file, a number of different predefined manuscript or script formats, etc. Scrivener does all sorts of magic for writing scripts, though I know nothing about that. There is also an outline mode which, in the Mac version, is very complex and powerful. In the Linux Version it is not. So I won’t mention it.

The compile process is cumbersome, esoteric, complicated, and requires training, so it is PERFECT for the average Linux user! But seriously, yes, you can compile your document into a pre-defined format in one or two clicks, but why would you ever do something so simple? Instead, change every possible option affecting formatting and layout to get it just the way you want it, then save that particular layout for later use as “My layout in February” or “This one worked mostly.”

The Powerful Compile Dialog Box.
The Powerful Compile Dialog Box.
One might say that one writes in Scrivener but then eventually uses a word processor for putting the final touches on a document. But it is also possible that you can compile directly to a final format with adequate or even excellent results and, while you may end up with a .docx file or a .pdf file, you are keeping all the work flow in Scrivener.

This fantastic and amazing book was compiled in Scrivener directly into ebook format.

You have to go HERE to find the unsupported and dangerous Linux version of Scrivener. Then, after you’ve installed it, install libaspell-dev so the in-line spell checking works.

A scrivener project file is a folder with a lot of files inside it. On the mac, this is a special kind of folder that is treated as a file, so that is what you see there, but in Linux you see a folder, inside of which is a file with the .scriv extension; that’s the file you run to open the software directly from a directory.

Do not mess with the contents of this folder. But if you want to mess with it you can find that inside a folder inside the folder are files that are the scenes you were working on. If you mess with these when Scrivener is using the project folder you may ruin the project, but if Scrivener is not looking you can probably mess around with the contents of the scene files. In fact, the Mac version gives you the option of “syncing” projects in such a way that you work on these scenes with an external editor of some kind while you are away from your Scrivener base station, i.e., on your hand held device.

Since this data storage system is complicated and delicate, it is potentially vulnerable to alteration while being used by the software, with potentially bad results. This puts your data at risk with cloud syncing services. Dropbox apparently place nice with Scrivener. I’ve been trying to figure out if Copy does, and I’ve been in touch with both Scrivener developers and Copy developers but I’m not sure yet. I use Copy for the masses of data on my computer because it is cheaper, and I use a free version of Dropbox for Scrivener files, just in case.

I would love to see more people who use Linux try out Scrivener, and maybe some day there will be a full Linux version of it. As I understand it, the Linux version is a compiled subset of the Windows version code base (yes, there is a Windows version) and the Windows version is a derivative of the Mac version.

I should also add that there are numerous books and web sites on how to use Scrivener, and Literature and Latte, the company that produces it, has developed an excellent and useful manual and a number of useful tutorials. Literature and Latte also has an excellent user community forum which is remarkably helpful and respectful. So be nice if you go over there.

How to write a computer book

I’ve designed an outline, which can be used as a table of contents, for a computer book about anything. In this case, about foo bar.

Preface
Forward
Introduction
Overview
What is foo bar?
Before you start
A brief history of foo bar
A longer history of foo bar
Why you want to use foo bar
Why you might not want to use foo bar
Alternatives to foo bar
Obtaining foo bar
Installing foo bar
Getting help on foo bar
Getting help on reading this book about foo bar
Alliterative methods of installing foo bar
Installing foo bar from source code
Installing foo bar from alternate binaries
Installing foo bar on dead badger
Why we wrote this book about foo bar
About the authors
About the reviewers
About the publishers
About the concept of “about”
How to download the code for foo bar
Typographical conventions used in this book
How to read this book in black and white
The plan of the book
What each chapter will tell you
How the chapters in this book are organized
A history of prior revisions and printings of this book
A word about this book’s font
foo bar basics
Advanced foo bar
Futher Reading about foo bar
Index

DR Congo #Ebola Outbreak

We can now be pretty sure that the Ebola outbreak in the DR Congo is not an extension of the West African outbreak. The index case seems to have gotten the disease from a mammal she butchered, and the numerous other cases seem to stem from contact with her primary as health care workers and family members. I don’t think we have enough information yet to assess this outbreak vis-a-vis the genetics of the Ebola itself.

From WHO:

On 26 August 2014, the Ministry of Health, Democratic Republic of the Congo (DRC) notified the World Health Organization (WHO) of an outbreak of Ebola virus disease (EVD) in Equateur Province.

The index case was a pregnant woman from Ikanamongo Village who butchered a bush animal that had been killed and given to her by her husband. She became ill with symptoms of EVD and reported to a private clinic in Isaka Village. On 11 August 2014, she died of a then-unidentified haemorrhagic fever. Local customs and rituals associated with death meant that several health-care workers were exposed and presented with similar symptoms in the following week.

Between 28 July and 18 August 2014, a total of 24 suspected cases of haemorrhagic fever, including 13 deaths, have been identified. Human-to-human transmission has been established and includes the health-care personnel who were exposed to the deceased pregnant woman during surgery (one doctor and two nurses) in addition to the hygienist and a ward boy, all of whom developed symptoms and died. Other deaths have been recorded among the relatives who attended the index case, individuals who were in contact with the clinic staff, and those who handled the bodies of the deceased during funerals. The other 11 cases are currently being treated in isolation centres.

The Keeling Curve

The Keeling Curve is the measurement of CO2 in the Earth’s atmosphere. As we burn fossil fuel or damage “Carbon sinks” we increase that number. The Keeling curve is at the root of much of the science of global warming. It goes up over time because of the release of fossil Carbon, and it wiggles up and down at shorter time scales for other reasons. For example, the curve drops during the Northern Hemisphere summer because the plants on the north side of the globe take in some of the CO2 and make it temporarily into plant tissue. During the northern winter the reverse happens. (There is a lot more land in the Northern Hemisphere).

Anyway, the Keeling Curve is now a movie! And you can watch it for free here:

Source

#Ebola: Second, possibly third outbreak, West African outbreak growing

The number of people known or suspected to be infected with Ebola in the West African outbreak is increasing, and the rate at which it is increasing is increasing. About 40 new cases are being reported per day on average, but the number of new cases has been going up by a few a day.

However, it is still unclear that these numbers represent what is actually happening on the ground. There is little confidence that the WHO has a good idea of who is currently stricken with the disease, and efforts to contain those who are have had mixed results.

A second outbreak is now occurring in the DR Congo (formerly Zaire). This is a second separate outbreak. So, it is NOT correct to say that Ebola has spread into the Congo. It didn’t. It emerged there independently.

What are the chances of that happening? I have long maintained that the conditions for Ebola spreading into human populations include factors that make the overall chance of that happening, for a large region, go up enough for multiple simultaneous epidemics to be more likely than chance might suggest. Perhaps I’ll discuss my reasoning for that another time. In any event, the DR Congo outbreak, about which we know very little so far, appears to be a different strain of Ebola, so this is not the Wester African Ebola spreading to Central Africa.

There are reports of a third outbreak of an unknown disease that might be Ebola also in the DR Congo. But that could be a lot of things. Including Ebola… so we shall see.

Also, there is one new case in Nigeria, after a period of several days with no new cases.

Should it be "math" or "maths"?

Do the math:

There are actually two answers to this question.

First, “maths” looks plural and is preferred by some because “mathematics” is plural. The problem with that is “mathematics” is no more plural than “physics” or any other compound noun. It is a rational sounding utterly incorrect argument. If we said “mathematics are cool” then there might be a case. But we say “mathematics is cool.”

Second, some people say maths and some people say math, and that’s how language works. That is a valid argument, but if you are walking around in the US saying “maths” instead of “math” be aware that you are demonstrating an anglophile affection, which is fine, as long as you know you are doing it. Please remember to demonstrate other anglophile affections such as referring to “English Muffins” and “Crumpets” and telling your friend “I’ll knock you up in the morning” when you merely intend to come by to walk to work together. Most importantly, if you have switched to “maths” from “math” because of some rational argument you once heard, just know there isn’t a rational argument. It is just a matter of usage. It is arbitrary. There is no readon. And if you are in the US you are using the non-standard usage. If you are in England or somewhere fine, talk funny all you want!

ADDED:

The conversation about “knocking up” has developed here, on Facebook and on Twitter. Interestingly a lot of Brits claim this is simply not a thing Brits say, yet it is. It may simply be patchy in its use, but it really is a British saying. More so than an English Muffin being a Crumpet (I know it is not, but I do love the reaction to the comparison among the Crumpet Sympathizers). Anyway, “I’ll Knock You Up” is defined in many places, and used by many Brits, to mean to rouse, wake up, call on, etc. another person. In American English, it means to make pregnant. In at least some forms of British, when does not “get pregnant” but one “fall’s pregnant” and if one chooses one might have the baby in the hospital, in America, or in hospital, in British-English areas.

Anyway, here’s the Google Ngram for various uses of “knocked”:

Honey, I Shrunk The Dinosaurs …

There is a fantastic paper just out in Science: “Sustained miniaturization and anatomoical innovation in the dinosaurian anceestors of birds” by Michael Lee, Andrea Cau, Darren Naishe and Gareth Dyke.

I want to talk about this research but if you really want to know more about it, don’t rely on me; one of the co-authors of this important paper is Darren Naish, who happens to be a stupendous blogger, and he has written the research up here. So go read that for sure, and revel in the excellent graphics. Meanwhile I have a few random thoughts….

READ THE REST HERE

Climate Change Documentary "Years of Living Dangerously" Wins Emmy

The climate change documentary, “Years of Living Dangerously” was nominated for two Emmy Awards. That was well deserved and fantastic news. But, frankly, with Cosmos also nominated for the same categories, no one really expected more than the nomination.

But, while Cosmos dis win in the “Outstanding Writing For Nonfiction Programming” category, and good on them for doing that, “Years of Living Dangerouslytook the award for “Outstanding Documentary or NonFiction Series.

Screen Shot 2014-08-17 at 11.45.36 AM

This is of course because it is a great, well done documentary. But I like to think part of this outcome has to do with people realizing the importance of climate change as an existential issue.

You can watch the first episode here:

You have to have Showtime to watch the rest of it, but it will be available on iTunes and as a DVD next month.

Tanganyika v. Tanzania

Tanzania is the name of a country in Africa. Tanganyika is, among other things, the older name of that country, more or less. It is a formerly used term that should no longer be used to refer to that country.

Wikipedia has this wrong on the indicated page on August 16th, 2014. Any wiki authors out there, please feel free to fix. I recommend changing the term “Tanganyika” to “Tanzania” and deleting the rest of the sentence.

Why not change this myself? Here’s why.