CloudMagic

I will review another non strictly related to research app.
Though sometime I think that apps like CloudMagic do a lot more to researchers than other apps,  say origin lab and so on.

Most old fashioned researchers rely on paper, they print pdf they annotate them they use post it and so on. To my view it's a idiotic way of doing things but I was born in the 2.0 age (as a 'researcher').

For example I use Evernote to save all my thoughts and images and so on, what in the paper age would have been a huge collection of un-searchable post-it now is one or two searchable (did I have to mention, backup-ed in 3 places, everywhere reachable... ) Evernote note.

Then I use Papers app by Mekentosj, to save all my pdf articles and books.
Finally for the sake of universal access, I save the Paper's library on dropbox and use whatever app ( compliant to the pdf format rules) to highlight and annotate pdfs.

Bravó, you say, now you have to solve the problem you tried to solve in the first place.
You want to find the note regarding that python new module you made, and the pdf with the guide...

Here's where CloudMagic magic, no pun intended, comes in.

On my iPad, where I read most of my papers (god bless the human-retina saving retina display), I fire up the cloud magic app and voilà I can search in dropbox Evernote and so on.

Do you use google docs because you are more open than me, do you also wanted to search you teammate email regarding the same paper, or tweet, or status update,  yes CloudMagic will also do that (and a lot more, actually find out here).

May you hate iOS, sometimes I hate it to, well CloudMagic is available for :

Mobile apps
May you hate mobile stuff,  it exists as a browser extension and a web version. Albeit less capable than the mobile counter parts.
Browser extensions




I have some complaints though, first one is that the web version does not open the notes in Evernote and it struggles with dropbox item previews sometimes.
But I'm sure those little nuances will be fixed really soon and a osx app is also in the roadmap.

I don't give ratings, but you must try that service. If you are worried with privacy, I'm not,  FBI and Matrix are always watching me anyway, not CloudMagic (find out more here).

If you want a primitive stand alone app for cloud magic just use Fluid app, this icon here and make your own standalone app, add a shortcut with Alfred app (say cmd-f) and go:





Enjoy a cold beer, you will lose way less time searching stuff around and will be more productive, good luck measuring that crazy neutrino's speed now!


Installing a complete, interactive scientific python environment.

A small guide to have all the interactive goodness of ipython, wrapped in a nice qt backend.
Tested on osx 10.8 and super easy to install.
The first step is to install epd free python distribution, which is a well maintained  distro with most of the basic scientific packages.
The cool thing is that once installed you will able to add even more modules with easy easy commands.

Let's start: 
  • Download EPD free   http://www.enthought.com/products/epd_free.php
  • check your .bash_profile  

  • If it looks like that or very similar (the last 2 lines are important) go head if not, comment or delete other lines pointing to python in some way (be careful, if you need them).
  • Install pip to the epd python you will super user permission 1    
  • Check that the path where pip is installed is the right one, and check the modules version, if you want update them:
  • Also, now you can extend easily your python modules with:
  • Download Qt 4.7.4 libraries and PySide libraries
  • Install the .pkg files
  • Now you are ready to rock the qt console:
    ipython qtconsole --pylab=inline
  • Try this small program:
  • You will get this:


Ready to rock. Open a cold beer!

Now, there is no easy way to backup your installed modules. But you can sim-link  to dropbox if it is large enough. I have yet to try that approach, though.

Let me know if it works for you.



1. [Why, super user? because the default epd installation is in the library folder,good or bad it's up to you. But I like to have it installed there.]

Updated Latex editor wars.

Update on this post, with sublime text2 .
A full review will come soon.
But texpad is still winning.

Review: osx Pop Clip

Small  and quick review of one of my favorite utilities for os-x.

This small program will make a pop up appear every time you select some text, by default it will just give you the possibility to copy and paste or cut.
Time saving ( no more command ⌘ + c, ⌘ + V or right clicking...), but it doesn't stop here because PopClip supports extensions.
You can add a lot of them and new ones are popping every now and then on the dev website (here).

The lens will search on google.com the highlighted text.
1-copy note to evernote
obvious send text by mail
2-google translate
3- text to speech (english only)
4 - send to osx note app
5-send to the terminal window
6-send to reminder app
7 word count
And if you select a web or email address :

Option to open the link on safari 

Option to send an email to the selected email address.

Small utility with a very small price and very very time saving in a lot of situations.

Try it for free here or purchase it here for, one beer or five well worth dollars :

Mac App Store link

New graphic

I have changed graphics and layout to make the blog more legible.

Loads of new content is coming, so keep an eye open.


Latex editor on the go!

Yes, texpad for the Ipad works, and it works very well with both cloud and local typesetting!

Don't try to write the new review of the review! It is meant for quick and dirty jobs!


Texpad for Ipad is out now!

I will review it as soon as possible, but for now I can say that I've been using the beta for a few months and it has been a good experience, but you have to keep in mind that after all it is still an iPad you're working with!



$8.99/£5.99/€6.99

News.

Long time since last post.
I this time I finally graduated and got accepted for a master in Nanoscience at the university of Copenhagen. I will move by the 2nd of august so there may be others delay in posting review and tips.

I also got a new iPad.

New reviews are coming:

a)mendeley for ipad
b)papers for ipad
c)latex typesetting on mobile

stay tuned


Excel to LaTex

I hate excel, but sometimes it is very very handy for small data manipulation, statistic and so on.
The biggest problem I always have is how to convert the tables to LaTex.
Yes obviously it is possible to do it manually but it is very time consuming.

But there are alternatives:

Excel / CSV to LaTeX Table Fragments Converter
link
You can copy and paste an excel, csv or whatever you want separated and it will add the  "&" to make the code inside tabular or table environment.
Very handy.
 Latable (windows only)


Get it here, by Alex A. Denisov. 

Latable interface



Latable is a windows utility that automagiccaly converts your excel tables into latex code, you can chose the ambient, borders whatever and you can copy then the corresponding LaTex code.


Each time you close it an error will pop-up, just click ok and relax !




Happy LaTexing to everyone

Texpad 1.3 Review



TEXPADICON


Texpad is my editor of choice for OSX.
Thus the review is somewhat biased, not because someone pays me, but because of how much I love this software.

I started using texpad back in version 1.2 and it was nice but not really worth every penny.
Then I had the chance to get in contact with the developers.
And here the magic happened. They are simply the best developer ever. They respond really fast, they do take care of your problems and so on. This is something every developer should do especially for paid software, yet rarely happens.
Texpad has recently hit version 1.3 brining new features and bug fixes thus making it worth every penny.
Now on the review.

1)Interface.
I like minimalism, it's no secret. Texpad UI is minimalist and thus I really love it. It's not as bare and ugly as the one of texshop, neither crowded and ugly  as the one of texwork or texmaker.
Also texpad as its own error console split in two part, the upper translates in human readable language the errors found and the lower part is the default log of the tex engine.






Lastly texpad has its own outline on the left , with beautiful monochrome icons for section, chapters and so on. It is beautiful and it doesn't distract from the writing.



Everything in the interface is really polished and consistent also I think that the single window interface is just right for writing with latex especially in a widescreen world.

2)features
Texpad has mostly all the basic features of a LaTex editor.
It also support pdf<->source sync by a click on the pdf to highlight the source and cmd+click on the source to go the relevant sentence in the pdf.
It has also a very useful auto-completion feature which comes in very handy because it can autofill the \ref{} and \cite{} commands.
As for typesetting it supports XeTex, LaTex, pdfLaTex and pLatex.
It has also syntax highlighting.


3)Integration
Texpad feels as native as ever on osx lion.
Not only the icon, and the interface are really native-feeling but also the fullscreen support and the life-saving autosave(apple calls it Version)feature of osx Lion.
It also support looking up word directly in the built in dictionary of osx both in the source view or in the pdf.


4)Future
at valletta ventures (their site ) no one ever sleeps.
Version 1.3.1 wil be out  with

  • Supports the Biber engine as well as the Bibtex engine
  • Many fixes to the makeindex typeset chain, including an option for typesetting with both makeindex and bibtex.
  • Improved support for VoiceOver 
and later version 1.4  will support global search, also in included document in your main latex document file.





Available on the Mac App Store.  (paid app)





Texpad 1.3 relased.

texpad 1.3 logo


It has been released on the app store the version 1.3 of texpad.


It is my favorite LaTex editor, and soon i will make an in-depth review of it, along with a comparison of its rival latexian.

For now I can anticipate that I suggest buying Texpad, for several reasons especially after this major update.


Available on the Mac App Store.

Beauty and truth in physics (ted talk)


Another video really worth watching.
I do still think that any B.Sc. in science should include a compulsory course on epistemology.
I guess that not only better future scientist can be created but also better human beings in general.


LaTex editors war!

UPDATE: Sublime text 2 with sublimeLATEX:
Sublime text 2 with sublimeLATEX is a bit more hard-core but super powerful.
Imagine a TeXshop on steroid, with user configurable everything.
Full review coming later, but it has two downsides:
1-doesn't support pdf to source clicks usually very useful
2-it costs a lot 60 usd and you have to install skim.

Yet, i love it.
Full review coming soon.



TeXShop
TexShop is the de-facto default LaTex editor for osx as it comes with the latex distribution.
It has a lot of pros as it is fast an light and really stable. It supports autosave and full screen. 
The downsides are mostly that at times is too bare, without bits and stuffs that make your life easier.
It has no navigator  which makes it really unfriendly to use for big files.
Lastly texshop creates a load of auxiliary files when typesetting you have the opportunity to trash them with a command, but in my opinion they should be trashed automatically as they create problems.
Oh and yes, it's completely free.


TeXmaker
Interface is by far the most ugly thing in the world.
But TeXmaker is what I call a Swiss knife for latex stuff. It has everything a newbie needs to start using latex, and it has the best error reporting console.
The structure viewer is ugly but clear and useful.
Unfortunately it doesn't support autosave and fullscreen of osx lion.
Another problem I have is the zoom in the pdf preview isn't fluid or easy.
Did I mention is also free ?

Latexian View in Mac App Store ($9.99)
Latexian is a strange latex editor because it blends a nice interface with a new approach that is live updating pdf preview.
The features of this editor are really complete as it features a navigator, code coloring and folding, code clips for automating the same code entries and code completion.
Code completion and the auto updating live preview are both a big pros and a cons.
In fact code completion is nice as it also features a nice description of the code you're entering but is not that easy to call as you have to use cmd+enter.
Navigator also gives you the opportunity to use your own bookmarks but if you want to know why it's not perfect read till the end of the post.
Also, autosave and fullscreen of osx lion are supported.


Texpad View in Mac App Store ($13.99 
Texpad is a good looking editor. I really like to think of it as the magic sentence "it just works" .
It may not have the same features of the cheaper latexian but it's a lot more lightweight, fluid and sable.
Actually the only features that are really missing as of now are code folding and lion autosave support.
Where texpad excels is in the autocompletion. Hit backslash start typing and voilà a semi transparent popup appears, scroll to the desired autocompletion hit enter once to complete twice to put also the corresponding closing coding. Autocompletion never failed thus making me focus completely on writing.

Navigator comparison:
I've found latexian's navigator to bee slow at times, moreover the non indented tree structure is not readable at a glance the black and withe indented tree structure  of texpad is gorgeous and useful. I'd say texpad has a "minimal" approach.


Who's winning.
The free editors are on par, it depends on you.
The two paid editors are both super nice editors and they are both correctly priced.
Choosing one of them is a matter of your personal taste, but Texpad is by far the best looking/working (save for a minor dropbox bug, that is being fixed) latex editor for mac.

osx LaTex editors Battle

Stay tuned for the ultimate battle:


Each software will be evaluated, for its UI, Workflow, stability, ease of use.




Mac os-X scientific Plotting software.

Curated list, without any sort of sorting but omitting those useless (in my humble opinion) buggy old software, ruled out are also command line based software(that is, without any kind of GUI). I'd say that the following software are the only ones ready to kick out of business origin lab dumb windows only stuff.


  • Plot, free to download here. Very capable but with a difficult to use interface.
  • SciDaVis, here, distributed as binaries manily a clone of the old origin 6.1 was't really stable in my test.
  • Igor Pro, my beloved workhorse, though a bit pricey  get a trial, or buy here
  • Magic plot, see my review, every mac-user researcher should have it. Get it here.

I would add matlab and wolfram mathematica to this list,  they both have plotting and data analysis, though they are rather over-complicated for daily and routinely stuff.

Know more, drop a comment!!


Did you know that..



Did you know that Google, with its very own google scholar service, has introduced a new feature some time ago.
Namely it has introduced "my publications" a very cool service that helps those who publish to find out where when and by whom they were cited.
As always you are being presented with all the statistical goodies that google had always used to delight us.

 An interesting review found here.






Papers 2.0 for windows beta relased.


Finally mekentosj has released a beta windows version of they fantastic papers reference  management software.

Go and grab a trial here.

The battle with free and fabulous mendeley is getting more and more interesting now!



MagicPlot review

MagicPlot 2.0 review 
More info and a complete overview of the features here: magic plot website.




Magic plot seems to be a rising star in the firmament of the data analysis and plotting softwares.
In this review I will show why you should use it and why you should support it.
First it's multi platform, maybe i will sound a tad obsessed, but in my view it's a very big plus.
Then it's very lightweight , very fast and very easy.


a)interface:


Default interface 

Yes it's a bit dull, but it's less overcomplicated than that of origin lab, and easier than the 
minimalistic one of igor pro! 
In the bottom status bar you see some details of what you are working on. (e.g the data you are hovering with the cursor, the x and y values, and the state of your project.
status bar
If you select a trace not only it will be highlighted with a green halo but the relevant entry in the legend will be also  highlighted. Very handy.


A minor glitch is that you can assign a label to a point, in wich the x,y values are shown unless you copy and paste the values manually. But the developer says that he's working  on it.


b)the fit interface:
As much as I love igor pro it is sometimes over complicated.
Magic plot offers instead a very simple, clean and easy fit interface.
But don't be fooled it's also a very capable fitting tool.
Fitting with a custom function.  
You can in fact fit with a custom function, or a sum of functions, or a function and a base line.


And lastly you have the tool to do a visual peak fitting adjustment.


Base line subtracted, manually adjusted gaussian peak fit.
There is also a fast fit interval selector, which is very handy.


And a report window, that offers a clear view of the fitting results.
Fitting report

c)data import
Importing data files is easy and fast even with big amounts of records.
From the import text table you can also set names, and preview your data plots.

I'm very surprised by how well the auto detecting of  both the column delimiter and decimal separator works. In my test, it never failed. NEVER.


Batch data processing is also on board, it worked very well in my tests.
 For an overview look on magiclplot site http://magicplot.com/wiki/batch
 
All sort of manipulation of data is possible, differentiating, integrating or setting persona formulae.

d)plotting
Plotting data is easy and straightforward, you can have multiple y over a single x, or multiple x,y.
Multiples axes are also available, as well as table-like axes and inset axes.
You can also save style templates, which is a super useful feature! 


Plots can then be previewed and exported in the most common and useful formats.

The anti aliasing and the vector quality of the graphs are very high, higher than origin lab and on par with igorpro!

Conclusions.
Magicplot has some incredibly nice features, yet one may assert that in comparison with origin lab or igor pro it's underpowered.  This assumption holds true only if one must do 3d plots, or over complicated things which require scripting or automating or if you have to use real time acquisition of data.
But in my opinion magic plot wins first for its balanced simplicity, it can do mostly everything and it can do it very fast.

First time I write something about price, but in this case it is a very important part of the review.
 Magicplot exist in a free fashion(but it has some limitation) or in a commercial version  which is 149$.

Origin lab or igor pro cost from 3 to 5 times more. And most of the times the support or the help files aren't even that nice or well put together. 

Considering all of the above,  magicplot gets 5 stars out of 5. I really suggest it to anyone! 









Next up : magic plot.

Magic plot, plotting and fitting software.

You  can get an overview of the major features on here: magicplot web site .

First feature that makes this software noteworthy is that it is cross platform  (win, osx, unix like).
It seems to produce very good quality graphs, and offers some unique management feature of traces in the graph window (i.e. you click on a trace, and it's highlighted with a green halo and the relevant legend entry is highlighted too.)

Screenshot of main interface with simple plotting going on.

Igor Pro review (2nd and last part)


Igor pro review.
(by wavemetrics , version 6.22a)

IGOR Pro is an interactive software environment for experimentation with scientific and engineering data and for the production of publication-quality graphs and page layouts.

Igor pro runs on windows and macintosh natively.
For a complete overview I suggest to browse wavemetrics site, linked above)


First part here

a) File import, and batch file import
Igor pro can import mostly all kind of text data files (e.g. data files, csv ).
The process in which data files are converted into waves is straightforward, you have the finest control over all the parameters.
The only gripe I have is that batch file import isn't easy at all.

b) graph printing
Graphs are very high quality and really better looking than most ( especially better looking that those printed in origin lab).
They can be exported in a plethora of format. (see picture)
Graph format export options

c) Summarizing:

Igor pro is really powerful, but at times it can be "scary" and unfriendly.
Main pros:
-really powerful if you master the igor pro language programming(most students really don't need all this horsepower)
-very clean  command based interface 

main cons:
-very clean  command based interface (Note: interface interaction can be painful if you don't master it enough)
-batch import of date files is awkward
-not available for Liunx distributions.


All in all, you have to carefully evaluate your needs and your habits.
 For simple plotting and data analysis igor pro may be a tad overkill and thus can drive you mad.
But for complex experimental procedures the flexibility of igor pro is unmatched.








A modern work approach: sharing and collaboration.



" Sharing knowledge is not about giving people something, or getting something from them. That is only valid for information sharing. Sharing knowledge occurs when people are genuinely interested in helping one another develop new capacities for action; it is about creating learning processes."

Cloud based collaboration and sharing can improve our research workflow.
Research in the cloud
  
Sharing knowledge,  think: papers,books(legally), images, graphs,  etc... , can really speed up the research process by cutting out dead wait times.
Why should you waste time to search for an article your mate has already found and maybe readed and summarized?
 You shouldn't indeed. That's why you must start by setting up in mendely, or papers, or zotero shared libraries.
Life will then be easier, no  links to send no paper to scan/fax pure and simple web 2.0.

Collaborating not only can speed up your work, but can also be stimulating and fun.
You can collaborate by writing with someone, or talking you your colleague what about real time collaboration on the same project?

I will now picture a modern work approach, by no means perfect but sure useful when mastered.


  • First: think about your needs.
  • Second: start using dropbox to have a drag and drop sync folder shared with those you want to work with.

In this folder make subfolders for any type of file (e.g. graphs, pictures, drafts and so on.)
(avoid chaos, see first point, think before creating useless digital stuff.)
Dropbox is free and fast and secure, and keeps the history of your files.
If your computer breaks, get stolen or other misfortunes no one will yell at you because all datas are safe in a fluffy cloud.


  • Third: collaboration office and latex.

In my view latex isn't really optimized or suitable to collaborative writing.
But you can always make a latex  project's folder shared in dropbox.
Since i consider latex typesetting only the final beautification step of the work collaboration isn't really relevant.

Office documents, mostly text and tables, can be optimized for collaboration.
Software nedeed:

  1. office (either open office or microsoft's)
  2. google documents account 
  3. If you have a mac then download Insync.
  4. If you have windows and Microsoft's office then download google cloud connect
    If you have windows and use open office or if you have Ubuntu than download  oo2gd .

    UPDATE: installation of oo2gd step by step look here.

All of these software work really well and plenty of tutorial will tell you how to set them up.
You can then start collecting data in a new spreadsheet and in the same time your workmate.
(For a simple explanation watch the video below)


You will end up with a shared papers library a collaborative environment and in the same time most of your precious stuff will be safe and ready in a could backup: no more data losses. 
And most of all, in a free and multi platform way.