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purchasing advice: computational biologist

M

mattsajay

macrumors member
Original poster
I am a computational biology student who wants to purchase a macbook.

I do moderate programming stuff (mathematica, matlab, maple, R statistical computing, c++, java, python and lisp) and some graphics (photoshop, imageJ etc). These are modest uses and not very high end like professional coders or image editing.

what configuration would you guys suggest for the macbook. my budget is around $ 1500 (with educational discount). of course i can go upwards max upto 2 grand if the deal is great. but preference is around 1.5 grand.

specifically,

1. is there a perceptible difference in performance for the above requirements between a 2.16 ghz and a 2gz chip

2. is a 2 gig ram sufficient?

3. has anyone made a dual boot system with mac tiger and kubuntu/suse linux

4. i keep getting mixed reviews about refurbished systems. any advice specifically for the type of job i will be doing (as mentioned above).

5. am i right in understanding that 2 gig is the max ram possible for C2D macbooks out int he market right now. (i.e. even if I buy ram 2x2 gigs later, i CANNOT upgrade my system.

i expect the notebook to last for 3-4 years till my thesis is done.

your inputs are greatly appreciated.
 
mattsajay said:
I do moderate programming stuff (mathematica, matlab, maple, R statistical computing, c++, java, python and lisp) and some graphics (photoshop, imageJ etc). These are modest uses and not very high end like professional coders or image editing.
Click to expand...
Those are actually not so modest uses. 🙂 Fortunately, the MB's are certainly enough for those tasks.
mattsajay said:
what configuration would you guys suggest for the macbook
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I'd recommend the middle-of-the-line one with 2GB RAM and all the disk you can afford.
mattsajay said:
1. is there a perceptible difference in performance for the above requirements between a 2.16 ghz and a 2gz chip
Click to expand...
Not really, but there's not a lot of price difference once you add things like a DVD burner, etc. to the low-end system.
mattsajay said:
2. is a 2 gig ram sufficient?
Click to expand...
Yes, based on what your usage is. More RAM is always better, but the MBs support 2GB max.
mattsajay said:
4. i keep getting mixed reviews about refurbished systems. any advice specifically for the type of job i will be doing (as mentioned above).
Click to expand...
I think they're fine if you don't mind a scratch or two, which you might not even have to deal with.
mattsajay said:
5. am i right in understanding that 2 gig is the max ram possible for C2D macbooks
Click to expand...
Yes.
mattsajay said:
i expect the notebook to last for 3-4 years till my thesis is done.

your inputs are greatly appreciated.
Click to expand...
As with any such purchase, wait until you need it, then buy it. There might be a new MB with a 3GB or 4GB max out soon. There might not be a new MB for 9 months. You never know. But, in general, what's there now is fine for your needs.
 
I am new myself, but I just wanted to say well done on the description of your requirements. You seem to really know what you need.

One thing I think you have missed however is your *social* and *enviromental* use.

Consider what you might want to socially use your *machine* for and also *how* and *where*.

Good luck in your search and studies.
 
I'm just as new as you, in fact I posted a list of questions just a day ago, but from the research I've done, if you go through the ADC (membership cost is $99) you can buy a MBP for a substancial discount (if you want a MB, then the educational discount is greater, and you want to buy applecare through the educational discount, not through ADC), then you want to buy ram from a source like crucial because apple ram is expensive. This will obviously go over your budget, but it's quite a deal for a MBP, just remember to wait for the SR upgrade (soon).
 
I just saw a refurb MacBook Pro for $1599 on the refurb site. I'd recommend it over the MB if (a) the additional connectivity (like Firewire 800) is important to you, and (b) the features like a backlit keyboard, faster 3D graphics, and screen resolution matter. You could add more RAM later.

I have an MB of my own and a MBP through work. The MBP's connectivity options and backlit keyboard, as well as higher screen resolution, make it very useful for work (I program).

The MB, on the other hand, is easier to carry around and is just as fast.
 
jsw said:
I'd recommend it over the MB if (a) the additional connectivity (like Firewire 800) is important to you, and (b) the features like a backlit keyboard, faster 3D graphics, and screen resolution matter. You could add more RAM later.

I have an MB of my own and a MBP through work. The MBP's connectivity options and backlit keyboard, as well as higher screen resolution, make it very useful for work (I program).

The MB, on the other hand, is easier to carry around and is just as fast.
Click to expand...

Thank you everyone for the responses so far.

1. Could you please explain what applications use the faster 3-D graphics that MBP has that MB does not. Does graph rendering (in say Mathematica, specially given that the new Mathematica just came out; or JAVA) get affected by the difference or is that mainly ofr video or games or whatever else. ((Am I right in understand that you are saying this because of the shared RAM graphics in MB versus not that in MBP?))

2. How much max RAM can be added to the MBP C2D, 2GHz? The chip remaining the same, is it 2Gig?

3. I am unsure at the moment about firewire connectivity. That is mainly used for data transfers (to storage units, in my case), right?

However, I have been reading up these forums on "future -proofing". Hence that might be a good idea.

4. What is your advise with respect to buying from Apple store online (either new or refurb)versus online enterprises like Amazon or Expercom (seen through dealmac) or macmall?

5. If I add new 1 gig RAM after purchasing 1 gig original configuration, what does it do to the warranty? In case there is some hardware problem, does apple replace or take care of the machine given that I have installed added ram in the system?

and finally,
6. Given that most of you have been on these forums for sometime, are there specific refurbished machines for MBP or MB that I should be wary of? By that I mean , say Gen 1 MBP had chronic problems of heating up, Gen 2 machines had problems with logic board etc. Can such generalities be figured out? I would avoid machines from such " batches" then.

Once again, your inputs will be greatly appreciated.
 
very nice thread. i am in market for pretty much the same thing!

i noticed that there is a promo going on about 100$ rebate on printers. i was thinking of getting a printer for 100$, selling it off locally and recover the money or at least a substantial part of it (other than the tax). and get the mail in rebate as well. So that the efective price of the notebook drops down by around a 100$.

my questions is: what are peoples impressions with apples rebate and special discounts? are they prompt? are there any compaints.

forum veterans please chime in.
 
To try and help answer some of these questions..

2. How much max RAM can be added to the MBP C2D, 2GHz? The chip remaining the same, is it 2Gig?
Click to expand...

Up to 3GB

5. If I add new 1 gig RAM after purchasing 1 gig original configuration, what does it do to the warranty? In case there is some hardware problem, does apple replace or take care of the machine given that I have installed added ram in the system?
Click to expand...

RAM is user servicable so it does not void your warranty. Also remember there are only two slots for RAM in the MBP (If I am not mistaken). Therefore if it comes with 1GB, it is going to be two 512MB sticks. Therefore to get 2GB you would have to buy two 1GB sticks.
 
If you are going to be programming, I would recommend you the MBP just for its larger screen. You are going to want to have multiple windows open and visible at the same time, so you are really going to appreciate the more screen real estate.
And one more thing, both the MB and the MBP supports 3 gigs of memory (even though apple doesn't say so), but the MB takes a slight hit to the graphics performance, as the RAM is no longer running in dual channel mode.
 
eyebeaz said:
Also remember there are only two slots for RAM in the MBP (If I am not mistaken). Therefore if it comes with 1GB, it is going to be two 512MB sticks. Therefore to get 2GB you would have to buy two 1GB sticks.
Click to expand...

The MBP comes with a single 1GB dimm, so he would only need to purchase a 1 or 2GB stick to increase the ram.

The MB (non-pro) comes with 2x512 sticks and would require replacing both to max out the ram.
 
NJuul said:
And one more thing, both the MB and the MBP supports 3 gigs of memory (even though apple doesn't say so), but the MB takes a slight hit to the graphics performance, as the RAM is no longer running in dual channel mode.
Click to expand...

Is that right? As i was going to the tech specs I was kind of wondering myself that given every chip/other hardware tech spec being equal, how can the two have different max RAM capacities?

streinrog said:
i noticed that there is a promo going on about 100$ rebate on printers. i was thinking of getting a printer for 100$, selling it off locally and recover the money or at least a substantial part of it (other than the tax). and get the mail in rebate as well. So that the efective price of the notebook drops down by around a 100$.
Click to expand...

Can this be done? If true, this will shoot down the effective prices by 100 bucks. Other members please comment.
 
hi matt,
fellow computational biologist here. what kind of work will you be doing?

most of the time, i see people creating toy models or prototyping algorithms on their laptops and then move to a cluster when running real data. for these "back of the envelope/computer" calculations, any current laptop apple sells is more than sufficient. (1+gig ram but i wouldn't sweat it so much past 2 gigs)

while i do like programming with a larger screen, chances are if you are doing an extended amount of programming, you're likely to be @ a desk with access to an external monitor. in a crunch, i've found virtual desktops to very useful

like someone else said previously, you should consider the social and environmental uses as well. its nice to have portability if you want to hit a coffee shop or to have at meetings.

i'm usually too lazy to lug my 15'' around, macbooks might be more portable. personally, i'm waiting for the ultraportable with no optical drive 😉

in a nutshell,
1. you don't need the latest and greatest, chances are your laptop won't handle the data efficiently anyway
2. 2gigs of ram is healthy
3. go for portability
4. i don't think you will be needing extreme graphics capability for computational biology
5. i've never heard or read of a problem with a refurb unit; if you do, exchange it immediately.
 
I got a MB 6 months ago -- the middle, C2D, 2.0 GHz, 1G memory, 80? G drive. It's a great laptop, which means that it isn't great for everything. 1 Gig of memory is a lot. It's enough to **run** all the programs you list, and will be overwhelmed if the **problem** you're working on gets too large. Photoshop is CPU bound -- it doesn't need a separate graphics card. The machine comes with two 512 Meg sticks, and you can expand one stick at a time if you want (so add 1 G for 1.5). You lose dual-channel memory access that way when the sticks are not the same size, which slows things down maybe 5%, not a big deal. Adding memory is easy, as is replacing the hard drive, and neither affects your warranty. With this model you can only put in 3 G (1G + 2G -- 2G sticks are still expensive), which is a limitation of the chipset. If the next revision goes to the Santa Rosa chipset (see threads) then you will be able to add 4G, or maybe more.

The basic 80 Gig drive is also a lot. It will be plenty until you start saving images and music. Rather than putting a larger drive in the laptop, I'd recommend getting a 250 or 500 Gig external drive -- you'll need backup, and you don't really need to carry around everything.

As for computing, the C2D is powerful, but not enough for real computation. For one thing, when the Macbook isn't loafing it generates enough heat to need its fan, and it goes from nearly silent to quite loud pretty quickly. Also when you're focussing on a problem you really want a desktop -- linked to a big cluster if at all possible. If you have that available, and use your laptop for what its good for, you'll be happy.

Peter
 
hhlee said:
fellow computational biologist here. what kind of work will you be doing?
Click to expand...

1. writing python routines for transcription factor binding site hunting.
2. c, mathematica and matlab codes for gene entwork simulation. differential equation based model solving.
3. microarray data analysis with R.
4. some image analysis from live microscopy data, some photoshop:

you know, usual computational bio routines!

hhlee said:
most of the time, i see people creating toy models or prototyping algorithms on their laptops and then move to a cluster when running real data. for these "back of the envelope/computer" calculations, any current laptop apple sells is more than sufficient. (1+gig ram but i wouldn't sweat it so much past 2 gigs)
Click to expand...

bingo! i will mainly be playing around with code and test out modules in that code prior to running the simulations(remotely) via a cluster. (linux based machines, super-awesome computing power). Thats why I said " moderate" programming in my first post.

the points about social aspects of usage and portability of the machine are very well taken. i kind of thought about the screen size as well, but in the end, i think when doing serious programming, i will end up hooking it to my external monitor in the lab.

observer said:
ather than putting a larger drive in the laptop, I'd recommend getting a 250 or 500 Gig external drive -- you'll need backup, and you don't really need to carry around everything.
.
Click to expand...

i do that right now. I absolutely agree that a desktop hooked to a cluster is what i need if i were to do only programming. however, i also intend to use the machine during travel for talks and presentations in conferences (say 4 times a year). So you could say that the purpose of this machien would be to do " back of the envelope calculations" as well as presentations, writing reports, organizing imporant lab data in a portable manner (i.e. all of the functions which are essential for a PhD student)

thank you all who commented. please keep them coming if you have more to say.

no one said anything about what streinro said about free printers?????
 
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