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OK, here’s the story so far: From the start when I switched to the Mac in 2006 I was amazed by Quicksilver and its capabilities. This program was magically finding the application you wanted, could create short chains of events, e.g. find a photo first and then send it via mail. All this was available right from the keyboard and for the experts these shortcut-like procedures were executed in split seconds compared to finding the mouse on screen, dragging from a to b etc, etc…

Since that time a lot happened: quicksilver is no longer under development and similar programs came up, being able to do things in a quite similar way as QS did, albeit everyone of those has its different advantages/disadvantages. Type “launcher” into the search bar of MacUpdate and you’ll get a variety of spin-offs that are more or less powerful. In this blog I’ll concentrate on comparing LaunchBar to its two main opponents: Quicksilver and Butler.

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So everyone in your block tells you that hotkeys are all the rage when it comes to real productivity, since your fingers are already on the keyboard… but then, if you are very uncomfortable pressing alt-command-X and then remembering the difference from alt-command-Y or alt-shift-X or….

Quite obviously, the idea of shortcutting certain tasks that are usually hidden in menus is a brilliant idea, but I guess no one would ever call this intuitive or easy to adapt to. Another problem: in a perfect world you have one hotkey for a certain task - and this is true for all other apps. So, no perfect world yet. Until you install the two software gems I am presenting here, that is.

1. Assigning custom shortcuts the Mac way: The first solution coming in mind is that you can define your individual shortcuts in the most intuitive way possible - and the app to this feature goes by the name Menu Master. Let me give you some examples how to use it:

- imagine your software has a fullscreen option (like a DVD player or a word processor, i.e. Word 2004) but no (or a weird) shortcut assigned to it. With Menu Master installed this is as easy as you could think: highlight the field in the menu you want to assign the shortcut for with your mouse and press the shortcut you define “fullscreen” in other apps - that’s it, the shortcut will work now in this app as well!

- Another example maybe most of you know: with command-delete you usually delete things in the finder, but for instance iCal has no preassigned shortcut for deleting entries. In my opinion deleting something should always be performed by the same shortcut, so highlight, pressing command-delete and that’s it… of course in iCal entries you can delete by simply pressing delete, but tell me how often did You try command-delete just because You’re used to it? I stopped counting

For more info on Menu Master (you can buy it for $10) click here.

2. What was that shortcut again? The second solution helps you stay on track with your shortcuts - is called KeyCue: this is how it looks like when it is switched on by the shortcut (default is pressing command for a while). This screen shows you, depending on the app you are using the shortcuts available - if you start pressing the shift or option key now the highlighting would change to the shortcuts in the list activated by command-option or command-shift, respectively. By finally pressing the activating key the window would disappear, having fulfilled its duty. What I am using many words for turns into seconds of your workflow assuring you to do precisely what you wanted to do.

Just let me finally comment on the congeniality of letting this window appear when you press the command key for a longer time: this actually should be the moment when you hark your brain for that darn shortcut to do this and that elegantly and fast. By displaying the reminder just moments after you started wondering, waiting might still be faster than fumbling with the trackpad, finding your cursor, pulling down the menu etc, etc…

To purchase or download a free trial of KeyCue, click here.

In installing the two aforementioned apps you should be able to adapt your intuitive idea of a shortcut into reality while, if your intuition changes, or you bluntly forget, there’s the time-saving reminder. One last comment: these apps are not freeware, I know, but as far as I overlook it, there is no cheaper alternative either and once having integrated these you’ll soon find them as indispensable and worth the money!

Communication develops into my most favorite topic, it seems - this time I want to talk about communication between Macs.

When I bought my new Mac Mini (after realizing that I would not have a hardware backup if my beloved Powerbook gets lost) the problem occurred almost naturally:

You got two Macs, which is a nice feature, but there are things that should be there only once - the calendar and the address book to name the most obvious ones… Let me guide you through the process of synchronizing your two Macs via ToMacs:

1. Connection: Since under Leopard internet sharing is a very easy task, a connection between the two was a breeze:

- Configure secure internet sharing (within the “sharing” button in your preferences panel). For this I had to activate AirPort on the mini in spite of it being connected to the net via cable. This nowadays allows me to basically use the mini as an AirPort station with my Powerbook! This is a cool thing on its own - without airport being able to connect to the net from anywhere… Quite a luxurious thing to have I’d say

- Recognized my notebook via the Finder after activating the AirPort connection between the two computers

- Upon opening ToMacs on the system you built up the connection from you should see both Macs in the leftmost sidebar - now choose the distant Computer and either check some check boxes for miscellaneous things to sync or under preferences configure Your own folders or apps to sync! That’s it! It works as a charm for my setup, the only thing bothering me right now is the fact that syncing is a new dimension of the word sluggish.

After a very thorough search over the internet I found busysync, which is very nice for ICal synchronization (my biggest syncing issue) but, well, limited to iCal… then for the address book there’s another cheap sync app (You get the idea)… ToMacs tries to solve all your syncing problems at once!

So have a look at ToMacs (website is in french!)…or download from MacUpdate… and if you have any additional remarks, please find me responsive and willing to answer any questions in the forums!

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.

The history of reading and writing involves paper now for over 2000 years - screens for about 80 years, television and cinema included. This actually is roughly overestimated, since computers became affordable and available only some 20 years ago. We can without doubt state that we have a very strong tradition on handling and organizing paper and are just starting off handling written information digitally.

In this new field standards are almost not available yet, but PDF, the portable data format established by Adobe is one of the globally accepted exchange formats available. One of the unique features of OSX is the system-wide support for pdf file printing.

How do You handle paper?

Many people right now go the middle way and collect data digitally while being in need of a hardcopy they switch to printing and annotating/summarizing. This system works well for a limited amount of data, that is, how many blank sheets you have to your disposal, how much storage space etc…

Eventually, you will either experience your limits of having an overview or space to store printed paper conveniently. What digital information storage can help you with is stretch both of these borders and free resources wasted by this process, no matter how much it actually is you need to handle. While space is a no-brainer the overview is created through having the information context-sensitively searched in no time for you.

If the paradigm of getting information has changed, wouldn’t it be nice having an app to keep it in one place, say, edit, comment and organize your paper digitally?

The app: Skim is one of the many pdf handlers around - so why use this and not Adobe’s reader or any other applications? Because Skim is not only handling pdfs but integrating indispensable features we all are used to from handling hard copy information.

What I normally do reading my hardcopy papers is highlight important information to return to them if I ever look at the paper again.

In skim you can choose just such a highlighter to accentuate important content, or you colorize whole paragraphs with a rectangle tool…You even can pick Your color for the highlighting! This additional info of course can be printed out for further handling, but it is not necessary.

For those of you having to organize bigger documents, the content of a pdf is fully bookmarkable while you have the option to also integrate a comment in the bookmarks.

Often I include a short summary or just some key words that are of importance to me in this specific article… in skim you can add either a note to any position in your pdf, similar to a sticky note… but you can integrate all the additional information entered by the user is not stored with the PDF itself but rather as a “layer” that is applied to the pdf file. This information is saved into the same directory as the pdf and is opened simultaneously when skim opens the document.

While being aware that this shift of paradigms will take its time it will be unavoidable - flow of information is speeding up, our brains will assuredly stay the same limiting factor they have been ever since. Obviously the organizing and processing until this point has to be simplified as much as possible.

Skim is a very valuable approach to try keeping pace with the development by bringing techniques we know from working with paper and pencil to the digital format. Give it a try and experience the beauty of having information in one place.

Download now from Sourceforge

This week T-mobile announced the numbers of sold iPhones since launch in Germany - 70,000 units. According to the company’s press release it was by far the strongest requested Multimedia phone available.

While this number sounds amazingly high for this short time period, taking into account that during Christmas season about 2.3 million units were sold sobers the enthusiast a little. The corresponding numbers for the same period of time were 190,000 iPhones (UK) and 70,000 (France).

Can we say that the iPhone didn’t meet its expectations?

The iPhone follows the profile of almost every new thing swapping over from America to us. Germans seem to be skeptic in the first place, and rather reluctant buyers.

There is another important point to consider. I really have no idea what reputation AT&T has in the US, but in Germany T-mobile is polarizing the crowd. It is popular making contracts with companies and business customers rather than youth and private customers.

This image originates in the history of the company: German Telekom, now simply called T-Com was the state phone company before they were “outsourced” into the free market when other companies wanted to have their share, too. Competition of course was very healthy and especially the mobile market established its own hierarchies. Telekom additionally had the problem still being a huge monster of a company - since they couldn’t match the prices of smaller companies on the rise, they went for big business deals rather than Mr. Small Customer.

Therefore a surely significant amount of German Apple fans reject T-mobile and thereby the legal version of the iPhone. Since there are ways of using a different network by manipulation of the system software supposedly you also find more jailbroken units abroad. Generally the prospect of not having a guarantee and having no support is a big Non- seller.

For the European market it seems very likely that the big conquest of the iPhone will start with moving to 3G in the second generation. Since 3G is essential for companies and T-mobile mainly serving these clients, this move should be a sure bet!

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.

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!