Comments for Bergman Lab http://bergmanlab.smith.man.ac.uk Tue, 30 Apr 2013 20:22:52 +0000 hourly 1 http://wordpress.org/?v=3.5.1 Comment on Formatting Figures for PLoS Journals with Illustrator on OSX by Stephen Curry http://bergmanlab.smith.man.ac.uk/?p=1788&cpage=1#comment-126645 Stephen Curry Tue, 30 Apr 2013 20:22:52 +0000 http://bergmanlab.smith.man.ac.uk/?p=1788#comment-126645 For what it’s worth, here’s a method that worked for me:

Figures were prepared at (close to) the desired final size and labelled in PowerPoint.

For each figure, I selected all the image components, copied and pasted into a new file in Preview. Saved this as a PDF and exported as a PNG at 600 dpi.

Opened the PNG in Pixelmator ($15 program from the App store), set the image width to the required width (8.3, 12.35 or 17.35 cm); set the resolution to 300 dpi.

Using Image > colour management… set the colour profile to ‘none’ (not doing this causes the images to fail in the PLoS submission system).

Saved as TIFF (with LZW compression).

]]> Comment on Formatting Figures for PLoS Journals with Illustrator on OSX by Gabriel Moreno-Hagelsieb http://bergmanlab.smith.man.ac.uk/?p=1788&cpage=1#comment-125581 Gabriel Moreno-Hagelsieb Sat, 27 Apr 2013 20:48:06 +0000 http://bergmanlab.smith.man.ac.uk/?p=1788#comment-125581 Besides the above, imagemagick’s convert has several other options. LZW compression is one of them. I tried with a PDF figure I have:

—–terminal—–
% convert -colorspace cmyk -density 1600 arrows.pdf arrows-cmyk1600.tiff
% convert -compress LZW -colorspace cmyk -density 1600 arrows.pdf arrows-cmyk1600lzw.tiff
% ls -lh *tiff
-rw-r—– 1 gmh staff 816M 27 Apr 16:39 arrows-cmyk1600.tiff
-rw-r—– 1 gmh staff 13M 27 Apr 16:40 arrows-cmyk1600lzw.tiff
—————–

Same resolution, much smaller hard drive footprint. :)

]]> Comment on Formatting Figures for PLoS Journals with Illustrator on OSX by caseybergman http://bergmanlab.smith.man.ac.uk/?p=1788&cpage=1#comment-125329 caseybergman Sat, 27 Apr 2013 07:19:29 +0000 http://bergmanlab.smith.man.ac.uk/?p=1788#comment-125329 Rosie Redfield has posted a related protocol using Gimp here: http://rrresearch.fieldofscience.com/2013/04/formatting-figures-for-plos-journals.html

]]> Comment on Formatting Figures for PLoS Journals with Illustrator on OSX by caseybergman http://bergmanlab.smith.man.ac.uk/?p=1788&cpage=1#comment-125328 caseybergman Sat, 27 Apr 2013 07:17:11 +0000 http://bergmanlab.smith.man.ac.uk/?p=1788#comment-125328 Gabriel Moreno-Hagelsieb noted on twitter (https://twitter.com/gaboentropy/status/327957634714050560) that to HiRes CMYK TIFF files can be created in imagemagick’s convert as follows:

$ convert -colorspace cmyk -density 1200 fig.pdf fig-1200cmyk.tiff

]]> Comment on Formatting Figures for PLoS Journals with Illustrator on OSX by caseybergman http://bergmanlab.smith.man.ac.uk/?p=1788&cpage=1#comment-125322 caseybergman Sat, 27 Apr 2013 06:58:55 +0000 http://bergmanlab.smith.man.ac.uk/?p=1788#comment-125322 Amy Lossie mentioned on twitter (https://twitter.com/Ilovepigenetics/status/327760101324759042) that converting from ppt to PDF, then importing into photoshop and saving as TIFF using the same settings also works.

]]> Comment on Formatting Figures for PLoS Journals with Illustrator on OSX by caseybergman http://bergmanlab.smith.man.ac.uk/?p=1788&cpage=1#comment-124903 caseybergman Fri, 26 Apr 2013 08:53:29 +0000 http://bergmanlab.smith.man.ac.uk/?p=1788#comment-124903 Aaron Darling pointed out on twitter (http://twitter.com/koadman/statuses/327669728975921152) that Adobe makes their Creative Suite 2 available for free: http://www.adobe.com/downloads/cs2_downloads/index.html

However, CS2 only runs on Macs running 10.6 or earlier since Adobe CS2 require the Rosetta Power PC emulator to work on Intel CPUs.

]]> Comment on Installing libsequence and analysis tools on OSX by Getting libsequence and Boost to Play Nice | Monkeyologist http://bergmanlab.smith.man.ac.uk/?p=1027&cpage=1#comment-111302 Getting libsequence and Boost to Play Nice | Monkeyologist Wed, 03 Apr 2013 19:12:53 +0000 http://bergmanlab.smith.man.ac.uk/?p=1027#comment-111302 [...] hint from this blog post. See also this nice tutorial on installing libsequence on Mac [...]

]]> Comment on Visualizing Biological Data Using the SVGmap Browser by SVGMap 1.5.0 released » Computational Oncogenomics http://bergmanlab.smith.man.ac.uk/?p=1887&cpage=1#comment-111179 SVGMap 1.5.0 released » Computational Oncogenomics Wed, 03 Apr 2013 13:18:26 +0000 http://bergmanlab.smith.man.ac.uk/?p=1887#comment-111179 [...] of gene expression and insertion preferention of transposable elements in the drosophila and have written up a useful guide about how to install and use SVGmap. As you also can read in the same blog post, they have [...]

]]> Comment on Compendium of Drosophila microbial symbiont genome assemblies by caseybergman http://bergmanlab.smith.man.ac.uk/?p=1851&cpage=1#comment-100034 caseybergman Thu, 14 Mar 2013 16:50:10 +0000 http://bergmanlab.smith.man.ac.uk/?p=1851#comment-100034 Paul Johnston on Twitter wrote:

@bergmanlab missed an Enterococcus faecalis draft (fly1) from the broad see http://t.co/UxhH6tuA and http://t.co/MV2IdiKM

https://twitter.com/Paul_R_Johnston/status/303136492799262723

]]> Comment on NCBI Blast Tabular output format fields by Xbello http://bergmanlab.smith.man.ac.uk/?p=41&cpage=1#comment-100009 Xbello Thu, 14 Mar 2013 15:31:40 +0000 http://bergmanlab.smith.man.ac.uk/?p=41#comment-100009 You have not, it opens by default in “r” mode, my fault.

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