Looking around the average scientist’s writing room, there is one thing you will certainly find: scientific publications, not one, two or 10, 20… depending on how much time you already spent working at this place, chances are good estimated numbers go in the five hundreds two thousands.

And we are talking real paper…

Until now it is very uncommon to have this organized electronically, out of the tradition of not reading on screen you do not organize papers (how everyone nicknames scientific publications) electronically but after you printed them. As introduced in my recent software review of SKIM, I predict that there will be a change in the way we are handling information, out of mere amount of information we are expected to juggle with nowadays.

Papers is a software that is able to help you remain in control of your virtual library- searching, archiving, exporting for bibliography in your publications, all these things can be performed with this suddenly very affordable time saver.

Let me explain how Papers is improving your everyday data mining and processing:

1. Getting the paper: you visit Pubmed, Google or any other depository and search for your topics or authors from within the program, save your searches locally, are able to very easily specify the search terms you defined: year, author, journal - the more precise you define your search term, the better!

These features are available through the website of Pubmed as well, but, be earnest, are you THAT common with it all that you remember the html tag for “first author”? I don’t and I am glad to have a frontend doing this for me while I can concentrate on the searching.

2. Handling the “piles of paper” - two points worth mentioning:

• importing the papers: you’d be amazed to watch papers tag your library- depending on how you saved the pdf upon importing about 2/3 of your stuff will be automatically recognized and matched to a fully searchable tag list! Matching a paper that is not automatically processed through this routine is equally easy: seeing the pdf you mark the last name of the first author, a pulldown will appear, you select “first author”. Do this with a couple of specific tags, first and last author should suffice.
• searching and processing: within Papers you search everything by entering information into the common search box- be it part of title, abstract or any author- if your library has the paper, you are presented with it. Finally you can organize the papers, similar to iTunes, into (smart) folders and export them for use in common bibliography software like Bibtex, Sente and Bookends.

The big thing with Papers is that even if you decide not to use the program anymore, your articles will still be organized according to the folder structure the program created: /year/author. From this point of view left alone to avoid duplicates it is nice to import all your papers and let them be organized.

Describing this award-winning piece of art I only touched the surface, so get yourself a copy and simplify your chase for information!

Licences of Papers are available for €29. For more information, visit the developer Alex Griekspoor’s website.

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written by madmacmat \\ tags: Alex Griekspoor, Papers

There was a time when to every machine that processed piles of data a Mac was attached, while the writing room was the dominion of the PC.

Myth (noun):

1. a traditional story

2. a widely held but false belief/a misrepresentation of the truth

There was this story about the reality distortion field that his Steveness can create to afflict the minds of people that watch him perform. The ugly truth is: Microsoft somehow managed to create something similar… Unlike Apple’s CEO they do not enhance their appearance (PCs are still mostly piles of ugly plastic) but rather alter the perception of the average PC user concerning Apple… just similar to the first sentence above, BigM. is somehow using the same arguments to defend its case for a decade now. I am sick of hearing these things over and over again - let me demystify you!

Myth#1 - Macs are specialist tools: Some lab equipment is still connected to sturdy G4s running OS9.22. Coming from PCs, people are bumping against a wall of ignorance that purposefully was meant to force people to “think different”. One button on the mouse only, the system structure completely enigmatic to someone being used to such intuitive things as C: being the system drive ;-)… Comparing the current cat with 9.2.2 You can hardly determine that it is the same operating system. What I hear most from people is the opinion perfectly describing OS9 while being ignorant about the development at apple.

In my opinion and experience I was fine with every task I was trying to do on a mac - not a single one needs to be performed in a windows environment! Time coming in this section here at Mactropolis I will review pieces of software that especially help you tackle the daily lab routine, so stay tuned and flood me with questions, please. My daring statement is: you will not need Windows on your Mac for doing your lab work, there’s an answer for everything to tackle! Moreover, some things you’d even PREFER to do on your Mac!

Myth#2 - Macs are only nice but pricy hardware: this is something I can agree upon at first - Macs are pricier than the usual desktop or notebook you buy - be it used or not. And this should make your scientifically trained synapses work. Not only does the company sell the stuff for a lot of cash, the used ones also are VERY stable in price while request is there. This could be because Mac users treat their stuff better…but on average you know mankind enough to tell that this can’t be it. Still, you pay a lot for design you say?

In my opinion: DO NOT LOSE your scientific instinct when it comes to Computers - give it an unbiased look and feel.

Wandering through the notebook sections of the big malls I see myself confronted with one material, predominantly: plastic- sorry IBM and sony, ENFORCED plastic. Now lay your hand on a Macbook pro - feel the reassuring coolness of the aluminium? This is not a mere design artifact, this is built to last! And I can speak for my sturdy Powerbook at least that where my previous notebooks lost the occasional edge of plastic frame, the aluminium just does not care. Nothing moves if it’s not supposed to. Form is not only for the sake of form like it is, but for a reason you might not have experienced yet.

But actually, this argument bothers me if it comes from a scientist or any other person looking for optimal performance. You don’t judge the quality of something by the mere looks. This leads to no longer comparing Macs and PCs on the looks level (let us assume that you do not detest the design on sight), but on the output level. Let me point out some things that were eye-openers for me, as small as they may seem:

1. Ever wondered how a life without viruses would be? Not worrying about connecting anywhere abroad still is perfect peace on a Mac.

2. You open the laptop, it is READY TO START WORKING in seconds - this still amazes me every time i am opening my Mac!

3. Restarts are “one time a week” - events, because installing and deinstalling does not require you to do so.

4. Since I am using my Mac the error is sitting in front of the Computer. A hard lesson at first this creates an indispensable trust in the system itself - VERY relaxing…

Myth#3 - My special software is not available on the Mac: This is the main issue most people have- you depend on exchange everywhere, not only in science. So in PC world you have all you need in a neat collection, so why change the running system?

In my opinion: I remember this ad from IBM - they showed one of those “computers” from the sixties filling half a bureau… subscripted with “never change a running system”… made me smile too, but it answers the previous “why”: to improve the current situation. And this is what happens if you dare… I don’t say trust me, I just want you to do a real comparison… All you really need is someone who asked this question and had an answer - thanks to the Mayor we have a forum now!

Nowadays you can make the switch by running a copy of Windows in parallel… either emulated or bootcamped… you can take your sweet time… but trust me I am right

Let me shoot back a question at you: what is the MAIN exchange format for information? I would say it is pdf before word, but others won’t. To have a native pdf generator has proven to be indispensible. No problems, no software to install, you wanna show someone what you have, print it as pdf and send it, print it as hard copy or present it to an audience - the looks will not be altered, period! Just as you would expect it to work.

Finally, the point for me is not to give complete for and againsts. Since I found my solution already, mentioning anything else here would be pointless. What I want to do here from now on is give a perspective to work better on a Mac. No matter whether you own one, plan to own one, or whether this is your first curious contact with the idea.

It is easy for you, being a scientist - depending on what you’re best at - compare and aim for quality - there will be no way of avoiding the Mac.

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written by madmacmat \\ tags: Macs in Science

People might wonder what my new column ‘Macs in Science’ will be all about, so I will try to give you a brief scope on what I want to discuss here… and what my idea was when the mayor talked me into this

So first of all: I am a Biochemist from Germany doing a PhD getting myself busy with everything molecular biology has to offer, excluding some weird mathematical stuff they nowadays do to so-called “big pile ‘o data” - studies like Gene arrays and such - count me out there. I am nothing more than the average computer using scientist - which is what you need to know. Firstly for not falsely thinking that I can answer all weird questions, secondly to know that I am just like you (but maybe a bit bigger), trying to kick my a** to make that degree - while also getting now more involved in the process of writing for Mactropolis.

What I expect my column to be about is what I am currently missing no matter where I have looked: a forum from a scientist for Mac-using/potentially Mac-using scientists. Maybe because scientists are a group of ignorants - in order to believe in what you do makes sense we really sometimes need to have a very - say - obscured views on life itself. I trust that you, are one of those who like getting as much interaction as possible in order to grow in many more dimensions than just mere knowledge.

But now enough of that, this is the software I am currently using / have experience with, so this’ll be what I want to introduce to You!

• Papers: amazing bibliography and search and storage All-in-one for (scientific) publications
• Prism: The way graphs want to be displayed combined with the way You want to enter graphs
• EnzymeX: Cloning part 1
• 4Peaks: Sequencer can make mistakes, right?
• Geneious: it is easier to name the tasks NOT performed by this program
• SerialCloner: Cloning part 2
• Cellquest Pro: For everyone working with a Cytometer from BD
• Flowjo 8: form and functionality at its best for Your FACS analysis
• PCalc: big small calculator
• Freehand MX: Desktop publishing– or– I got the data and I want to publish them– what next?
• Micromanager: seeing is believing

Obligatory excursions towards general apps in science:

• Pages in scientific application
• Numbers in scientific application
• Keynote in scientific application
• Safari in Science
• Mellel with Bookends: the dreamteam for Your thesis?
• Scrivener Gold gathering and writing in one place.
• OmniFocus: How not to lose control over Your schedule.

I am already looking forward to each of these topics, so stay tuned!

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written by madmacmat \\ tags: Macs and Science