"Biological Science Journals need a reality check" written by Tinypliny on estrip.org

11/16/11 02:12 - ID#55525

Biological Science Journals need a reality check

I read this article today (poorly written and not very informative. Don't bother reading).

Tchantchaleishvili V, Schmitto JD. Preparing a scientific manuscript in Linux: Today's possibilities and limitations. BMC research notes. 2011 Oct;4(1):434+. Available from:

.

The table at the very end summarizes the format in which top biological sciences journals prefer to receive submissions.

New England Journal of Medicine(34) PDF*, DOC, WPD, TXT, RTF
Cell(37) DOC, RTF, TXT
The Lancet(38) DOC
JAMA(39) DOC, WPD
The Journal of Biological Chemistry(35) PDF***
Circulation(40) DOC, WPD
===
Nature(29) DOC, TEX**
Science(30) DOC, TEX**, RTF*
PloS ONE(31) DOC, TEX, RTF
PNAS(32) DOC, RTF, TEX
BMC Journals (33) DOC, RTF, TEX

[* Some restrictions apply]
[** TEX files must be accompanied by a PDF version of the same text for visual reference 19 ]
[*** Although manuscripts must be submitted in PDF format, Microsoft Word is recommended to prepare the manuscript text]

Look at the sheer proliferation of M$hit formats on that list. The 1st preference is always doc. Wherever PDF is accepted, M$hit is recommended to make that PDF.

Even if you want to change *they* will not let you.
Ugh.

Am I in the wrong field or what? Nevermind content, even submission guidelines are so proprietary, backwards-thinking and insular.

Permalink: Biological_Science_Journals_need_a_reality_check.html
Words: 209
Location: Buffalo, NY
Last Modified: 11/16/11 03:15

Category: linux

11/16/11 07:35 - ID#55521

Undo any last action in Linux?

Sometimes, I accidentally move files into folders. However, I am uncertain what files I moved (because I wasn't paying attention when my stylus accidentally dragged and dropped that file into some nearby folder). So I know that something has changed in the directory but I am not sure about what has changed. In windows, I could easily right click and undo whatever the last action was - rename/delete/move. Where is this undo functionality in Linux??

If there isn't a way, is there at least a log that logs all these events so I could check it and see what was changed?

Am I missing some obvious way to do this? Ctrl-Z does not cut it.

tinypliny writes at 09:59:05 11/18/11 - Comment #66278: data exceed the size of the drive

this must be my dumb and dumber day... I have no idea what you are saying!!? If you start copying 10 gigs of data into a drive of say 4 gigs, it gives you a warning that the drive space is inadequate. Copying stops with a small buffer of space remaining on the destination drive. If you undo all this the copies files are just deleted.

paul writes at 09:38:13 11/18/11 - Comment #66273: I still dont' see what happens when the data exceeds the size of the drive. I get it with moves but not copies. I guess it probably works most of the time if directories never meet that condition.

tinypliny writes at 09:26:31 11/18/11 - Comment #66272: Its exactly like the undo option in chrome or any word processor for text. All recent actions in a session are potentially un-doable.

I think you are thinking about linux when you ask this because linux assumes you are smart enough and know what you are doing and there are no step-backs. But when your stylus is either a) not very precisely controlled (because your stylus company just doesn't care about linux enough), or b) maybe its too sensitive and you sneeze moving some folder inadvertently because you are in the nautilus gui, you have no way of knowing what changed...

It doesn't happen often but it does sometimes and is agonizing without an undo option. I posted in Ubuntu forums where people actually bother to answer and someone told me that Dolphin (KDE's file browser gui) has the undo option.

tinypliny writes at 09:20:31 11/18/11 - Comment #66271: % then a program started to fill your drive

I am not sure I understand this bit. If you copy a folder with gigs of data, you can still undo it. Windows will just delete the copy you made. Every time you do a rename, delete, copy or move anywhere, the context menu item for the corresponding undo rename, undo delete, undo copy or undo move becomes active and you can immediately go back to the original state. In any one session, if you have several such actions, ALL of them can be undone one by one stepping backwards.

paul writes at 09:14:22 11/18/11 - Comment #66269: I dont even understand how undo could work under all situations. Say you copied a folder with gigs of data, then a program started to fill your drive, then you undo? What happens?

tinypliny writes at 08:34:40 11/16/11 - Comment #66197: Nautilus is an awful file browser. Compared to the one in windows, it really feels like it came from the 1980s.

paul writes at 08:10:18 11/16/11 - Comment #66196: I never do anything with Nautilus or the GUI so I have no idea. I don't think there is a way.

Permalink: Undo_any_last_action_in_Linux_.html
Words: 117
Location: Buffalo, NY
Last Modified: 11/16/11 08:35

Category: buffalo

11/15/11 08:49 - ID#55520

Ikea proxy in Buffalo

Ikea might have turned down Buffalo but two canny blokes from our city spied the Ikea-craziness haunting everyone's eyes and decided to do something about it. Take a guess? No, they didn't rush out and buy mass tranquilizers to shoot at everyone. Your guess was fun but thankfully, wrong. The truth is less dramatic. They set up a website called myikeaplace dot com instead.

And how did I know about this charming entrepreneurial story? They left no apartment building behind. I have been seeing their flyers and hearing hushed whispers about my ikea place dot com ALL over my building, and beyond today. I can even hear the lady who hangs out in the balcony in the next building (a.k.a, beyond) smoking like a chimney and talking about it.

So I had to go and check out their website and it is quite an interesting business model. You just submit your ikea orders on their website. They go all the way to Pittsburgh, do the shopping for you and bring back whatever you wanted with them. You can then go fetch whatever it is you ordered in your ikea-craze from their ~~garage~~ professional storage rental on Ellicott.

What a nifty idea... I think I can definitely push my rickety cart from their warehouse to my flat. Maybe I should stop bitterly stalking the ebay seller who ditched my sale and get those LED lamps I want from our very own buffalo ikeamongers.

Permalink: Ikea_proxy_in_Buffalo.html
Words: 244
Location: Buffalo, NY
Last Modified: 11/16/11 09:05

Category: goals

11/15/11 08:32 - ID#55515

The 20 Times Tables: 18

Continuing the "mastering first grade when you are in graduate school" series.
The 18 table.

Starting with 18
36
54
72
90
108
126
144
162
180 -20 + 200
198
216
234
252
270
288
306
324
342
360

Permalink: The_20_Times_Tables_18.html
Words: 17
Location: Buffalo, NY
Last Modified: 11/15/11 08:32

Category: music

11/14/11 11:14 - ID#55513

Surgical

detachment?

1.42 minutes of Celldweller awesomeness

Permalink: Surgical.html
Words: 9
Location: Buffalo, NY
Last Modified: 11/14/11 11:15

Category: r statistics

11/14/11 03:09 - ID#55510

Where is R installed on Linux?

Simple yet frustrating question for those who want to view the code behind the base functions.

whereis R

Turns out R on linux is installed in the following directory structures:

/usr/bin/R : this is the executable binary
/usr/lib64/R

ls

bin COPYING etc include lib library modules NEWS NEWS.pdf SVN-REVISION

/usr/include/R

ls

Rconfig.h Rembedded.h R.h Rinternals.h Rversion.h
Rdefines.h R_ext Rinterface.h Rmath.h S.h

/usr/share/R

ls

encodings java library licenses locale make R sh texmf

/usr/share/man/man1/R.1.gz : possibly the manual pages

Permalink: Where_is_R_installed_on_Linux_.html
Words: 100
Location: Buffalo, NY
Last Modified: 11/14/11 03:18

Category: goals

11/14/11 02:27 - ID#55509

The 20 times tables: 19

I cannot believe just how AWFUL I have become at my 13 through 20 (times 20) tables. Struggling with mental arithmetic is totally unacceptable. It is a sign of mental deterioration that I want to fight against.

Starting with 19
38
57
76
95
114
133
152
171
190 +190
209
228
247
266
285
304
323
342
361
380

Permalink: The_20_times_tables_19.html
Words: 36
Location: Buffalo, NY
Last Modified: 11/14/11 11:51

Category: linux

11/14/11 01:30 - ID#55508

Ctrl-L is for Location

I keep on forgetting this ridiculously easy shortcut.

Ctrl-L is for Location
-- in chrome
-- in Nautilus

Now, where can I find more RAM for my foggy brain?!

Permalink: Ctrl_L_is_for_Location.html
Words: 29
Location: Buffalo, NY
Last Modified: 11/14/11 01:30

Category: linux

11/14/11 12:56 - ID#55507

Display Full Directory Location in Nautilus

Nautilus in Gnome 3 has this annoying main toolbar with just buttons displaying the current directory you are in. There is no option to switch the display to the complete text version of the location of the directory.

Well, as usual, there is a round-about way.

Type:

Alt+F2

Run:

dconf-editor

In the dconf-editor menu:
Location Bar options are stored under

"org âžœ gnome âžœ nautilus âžœ preferences âžœ CHECK always-use-location-entry"

Whew. I am glad I can see precisely where I am and copy and paste locations into the terminal once more instead of staring clueless at the vague "pretty' buttons. I remember that when Gnome was in version 2.x, they had the option to change the location display format right under the preferences section of Nautilus.

It's somewhat cruel to take away the means to easily change display format options from an application like Nautilus and hide all of it under system configurations ONLY accessible by installing the dconf-editor.

Ugh. What were the Gnome 3 developers thinking??

Permalink: Display_Full_Directory_Location_in_Nautilus.html
Words: 162
Location: Buffalo, NY
Last Modified: 11/14/11 12:56

Category: tourism

11/13/11 04:59 - ID#55500

On the handmade path

Some of my favourites from back when the sun was not actually a big fat dazzling liar.

This brilliant brittle white mushroom bunch looked like it had to be saturated with some calcium salt. (e:matthew) and I wondered about the source.

Contrast that with this one - possibly filled with iron salts or rust.

It was such a happy day! Behold the cutest smile on the planet! :)

(e:Paul) taking the panoramic shots...

These great rotting branches reminded me of my muscle dissection days.

We plodded through a rustic-looking huge open field of fluffly little dandelion-like plants. We had fake "snowball" fights and all the little fluffy things ended up attacking me. I think (e:YesThatCasey) totally incited the attack.