Wikipedia:Reference desk/Archives/Computing/2014 January 20

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January 20

Ubuntu in VirtualBox

Hello! I am trying to set up my Windows Server 2008 (among other things). I installed Oracle's VirtualBox and it seems to be working more or less OK. Then I tried to install Ubuntu Desktop. I downloaded it, unzipped it with UltraISO, copied the whole directory on a DVD, burned it and used the executable file there to install the OS. I hoped that somehow it will end up as the Guest OS in Virtual Box but this does not seem to be the case. It appears (I may be wrong) that it is now a third OS on this computer because I see it on Windows Boot Manager (black screen). I have now Windows Server 2008, Windows 7 and Ubuntu there. What did I do wrong and how to correct it? Thanks, --AboutFace 22 (talk) 01:44, 20 January 2014 (UTC)

It sounds like you have indeed installed Ubuntu directly onto your hard disk as a third OS alongside your two Windows installations. You probably now have the option to choose Server 2008, Windows 7 or Ubuntu at boot time. Unfortunately, you cannot switch between them without rebooting.

Ubuntu is not installed in the virtual machine (Virtualbox). To install it, you first need to create a virtual machine. Virtualbox supplies a few configurations (including one for Ubuntu) for you to start with, or you can create your own from scratch. Make sure your VM is created sufficient virtual hard disk space and sufficient memory - this suggests a minimum 5 GB disk space and 500 MB memory], though you will almost certainly want more if you want to run anything other than just the OS. Once configured, start Virtualbox and then start your virtual machine. The virtual machine's BIOS will detect that no OS is installed and at that point you tell it to look at the Ubuntu Desktop ISO file you downloaded or or the DVD you created. It will install Ubuntu to its virtual hard drives and then you're done.

As for removing your triple-boot Ubuntu from your hard drive, that is quite easy though you might have to do something with the Windows Boot Manager - I'm not sure what (maybe someone else can help with that). Astronaut (talk) 12:23, 20 January 2014 (UTC)

Thank you. I did create two virtual machines in VirtualBox: Windows 8 and Ubuntu BEFORE I installed UBUNTU from the DVD. It was easy. Unfortunately it did not give me that option you describe. I sort of expected it but it never appeared. I will try to read literature more closely. Ubuntu now appears in the Boot sequence and also as a program installed in Windows Server. It is in Control Panel==>Uninstall Programs. Thus it can be removed. Besides I know how to do BCDedit. I've done it many times. --AboutFace 22 (talk) 15:53, 20 January 2014 (UTC)

A virtual machine in Virtualbox is like a separate machine with its own BIOS, its own (and initially empty) hard disks, its own memory, etc. I recommend you read the manual - particularly '1.8. Running your virtual machine' - to read how to install an OS in a virtual machine. There are also video tutorials - just search on Youtube. Astronaut (talk) 18:53, 20 January 2014 (UTC)

Thank you, Astronaut. It is all very useful. --AboutFace 22 (talk) 02:31, 21 January 2014 (UTC)

How to find out if this tower has an OS?

typing on phone, sorry for grammar etc.

My boss wants me to get an old tower in working order. its a dell inspiron with a Vista sticker. When i crank it up, it warns me that the hard drive selfchecker has detected a possible problem with the hard drive. ging forward takes me to the Dell splash page and the Windows XP (?) splash page before it tells me Windows didnt shut down properly, would I like to start in safe mode, safe mode with network, safe mode with command prompt, last known working settings, or normally? All do the same thing; load for a while then loop backto the hard drive warning. doing a dell selfcheck with f12 fails because it cant find the partition. there is nothing in the cd drives.

I suspect there may be no os installed. how would i go about testing this? hoe do i fix it if he doesnt have the disks handy? wat else might be the problem? and why does a vista computer haven XP splash page? --Ye Olde Luke (talk) 09:11, 20 January 2014 (UTC)

If the XP splash screen displays there was/is at least 1 OS installed - i.e XP. Could be a dual-boot system but I would guess that it was downgraded from Vista to XP. Easiest way to check the drive is to remove it from the tower and plug it in another (working) tower or USB housing. Download Seatools (or whatever is appropriate for your brand of HDD) and run the diagnostics. Run chkdsk x: /r from the command prompt (where "x" is the applicable drive letter for the drive). If all goes well you should be able to browse the drive and partitions. You will be able to tell from the folder structure if it is XP/Vista. If there is more than 1 bootable partition you will need someone other than me to help you. The first step is to establish if the drive is not fubar otherwise you're wasting your time.196.214.78.114 (talk) 10:14, 20 January 2014 (UTC)

Another option which should at least get you to the point where you can look around for what the problem is would be to use a Ubuntu LiveCD/USB stick. It's a free operating system that will let you run the operating system off of the usb/livecd without trying to install anything. It's pretty easy to do, even. Without the Windows discs this may be the best way. And, of course, you could always install Ubuntu or another Linux distribution instead of Windows to avoid future problems caused by not having the discs (or by not having an up-to-date operating system). Regardless, I would also recommend running diagnostics on it. Even if you format and reinstall the OS you could still have hardware issues (e.g. a bad hard drive). --— Rhododendrites ^talk |  15:01, 20 January 2014 (UTC)

Since I don't have a second tower I could easily plug the harddrive into that isnt currently in use, I'm going to attempt the Linux workaround just to get inside the machine without having to take it apart. Any recommendations on diagnostics I should prioritize once I'm in the system? I figure harddrive-related things are the most obvious target.

Also assuming this doesnt work and i have to insert the harddrive into a new tower; the second tower won't be in danger right? Do hard drives just work in any tower, or do I have to keep the same make/model/providing company? Just dont want to take out another company computer. --Ye Olde Luke (talk) 16:04, 20 January 2014 (UTC)

Is there something special about that tower? Otherwise this seems like an incredibly inefficient way for your boss to use the salary you are being paid. Looie496 (talk) 16:21, 20 January 2014 (UTC)

Despite my degree in Literature, I'm known as the office 'tech guy' and all technical problems are directed to me. I just fixed the printer, remapped the network and am currently installing drivers for a scanner, with only Google, logic, and you guys helping me out. Thank you I should add :) --Ye Olde Luke (talk) 19:16, 20 January 2014 (UTC)

You're obviously a techie ;-). But the point is that a reasonable tower sells for about US$500, so unless you are very cheap or "there anyways", from an economic point of view, you should probably not fix machines that take more than a small single-digit number of hours to fix. --Stephan Schulz (talk) 20:05, 20 January 2014 (UTC)

I think i may have found the problem. i got ubuntu up and it works fine. followed these steps http://askubuntu.com/questions/317241/can-i-use-ubuntu-to-diagnose-hard-drive-or-ram-problems-in-windows but according to disk utility there is nothng under local storage. there are just no options except peripheral devices. oes that mean there is no OS installed? --Ye Olde Luke (talk) 20:22, 20 January 2014 (UTC)

No, that would mean it doesn't see a hard drive there. Might be a controller issue, might be a hard drive issue, but almost certainly not an OS issue (at least that wouldn't be your only issue). My instinct would be to tell you to run GParted rather than the Disk Utility to take another look, but that may just be based on my preference. At this point, now that you're [at least temporarily] a Ubuntu user, I would point you to the quite active and generally very helpful Ubuntu Forums, which will have a lot more OS gurus than frequent here, I think. --— Rhododendrites ^talk |  21:14, 20 January 2014 (UTC)

GParted agrees that the only partition is the one on the computer thumb drive. I admit to being slightly out of my league here, but I guess tonight I can ask the Ubuntu forums for help and see what they can do. Any further advice or recommendations on actions to take, let me know. Thank you all for helping me get this far :) 50.43.130.15 (talk) 23:04, 20 January 2014 (UTC)

Oh I thought you had nothing listed under local storage other than peripheral device (usb/cd). What is the partition "on the computer?" --— Rhododendrites ^talk |  23:16, 20 January 2014 (UTC)

Typo...I meant "is the one on the thumb drive." The Linux one I just added. 50.43.130.15 (talk) 23:53, 20 January 2014 (UTC)

It is sounding like either the disk controller is faulty, or much more likely the hard disk is faulty. You can check if it is the disk controller by trying a spare disk you probably have laying about - with an XP-era PC you probably don't want to buy a new disk just for this test. Assuming the disk controller is OK, you might want to talk to your boss about the usefulness of getting a new disk versus getting a new PC. As for the old disk, unless there is something critical on that disk I would suggest binning it, though do bear in mind your employer's disposal policy for such things. Astronaut (talk) 17:01, 21 January 2014 (UTC)

Yup, disk controller worked fine. Looks like there's something wrong with the hard disk. There's nothing important on said disk so I'm probably going to recommend he replace the hard disk. Unless I can find a way to get a factory restore through, so far I haven't found anyting that works except f2 and f12, both not very useful. — Preceding unsigned comment added by 50.43.130.15 (talk) 18:39, 21 January 2014 (UTC)

You really need to do the maths on the costs for this; like Looie and Stephan above, to me it looks like really bad financial sense.

• first you'll have to buy the replacement HD; at this age it's probably SATA, but it may not be able to use all of a modern SATA disk
• but then it doesn't have an OS; without the Dell recovery partition, you'll have to get a recovery disk from Dell (if they still have one for this model), for which you can get here
• now you have an ancient version of Vista; you'll spend half a day downloading and installing all the patches that have accumulated since the disk was authored
• at this point you have a working PC, with no software. Presumably you want Office and maybe something specialist (accounts, whatever). So you have to install that too, and (depending on what you need) pay for licences for it.

At the end of all that you have an old, slow machine with a poor OS. Based on the timeline of Windows Vista, this machine is probably 5 years old or more. Accounting wise it's written off - it's essentially worthless; getting it working won't make it worth anything. It would be one thing to resurrect this thing if you needed important business information off the disk, or if (perhaps for some obscure compatibility problem) you needed a reliable Vista machine. But if you just need a working desktop machine for someone to work at, this thing is a dead albatross. -- Finlay McWalterჷTalk 00:52, 22 January 2014 (UTC)

I don't think that there's been any mention of what the computer is (or might be) for. I presume that it's not for playing games. If it's also not for video editing or similar, it may be be up to whatever jobs there are. I routinely use a laptop originally marketed for XP. (I have to carry it around a lot, figure that if I'm going to drop and smash a computer then it might as well be the one with the lowest value, and use it for little more than displaying web pages and text editing.) A new replacement would look prettier, have a battery that wasn't a bad joke and would weigh less; it would have no other advantage that I can think of. Discarded computers don't vanish; they end up on trash heaps in third-world countries where they pollute and kill. So my congratulations to the boss for their reluctance to add to the trash. What to do with the computer? If I were in charge I'd install Crunchbang Waldorf (Youtube video) on it. This is what's running on my old laptop: quick, unproblematic, supported by a forum with helpful people (not that I've needed any support in months). Morenoodles (talk) 05:59, 25 January 2014 (UTC)

Focal Adhesion Counter

Hello. I count focal adhesions on about 200 photos a week with ImageJ. Is there a program that can automate this process so I do not need to manually contour the cells on my photos, measure the area of the contour, and summarize the number of focal adhesions? Thanks in advance. --Mayfare (talk) 23:28, 20 January 2014 (UTC)

For something as specialized as this, the only hope is to ask around among people who do similar work. Looie496 (talk) 03:33, 21 January 2014 (UTC)

Well you may be in luck - while I haven't worked on such things myself I have several colleagues who do automated microscopy analysis of cells and whom I could ask about this. The first thing you need to think about though, is how you define a focal adhesion in your images in terms which a computer can understand (i.e. absolutely specific and precise). You must precisely define a set of criteria that segregate the images fairly exactly into "focal adhesions" and "not focal adhesions". For example, what stainings do you have? Are focal adhesions in your images areas of colocalisation between two stains, do they have a maximum and minimum size, are they a characteristic shape etc.? You also need to contour your cells, but that is an easier problem as it is such a common thing to do that lots of pre-existing solutions exist.

The reason I am asking all this is that there are lots of programs which automate microscopy analysis, but they all have different capabilities, so I can't recommend one unless I know exactly what you want to do. If you get back to me with a) what your images are (are they 2d or 3d, confocal or wide-field, what stains do you have?) b) How you define both cells and focal adhesions, I can ask my colleagues whether they think any of the programs they are familiar with can possibly automate your analysis (a definitive answer is not possible, as so much depends on the quality of the data). A final word of warning; programs for advanced microscopy automation can be powerful, cheap or easy to use, and if you're very lucky indeed you get to pick two out of three. You may end up needing to spend many thousands of dollars if your requirements are sufficiently advanced . Equisetum (talk | contributions) 11:42, 21 January 2014 (UTC)

Hello, Equisetum. My images are 2D, wide-field, and stained with anti-vinculin and phalloidin. I define a focal adhesion as any streak (or dot) between 1 and 8 μm² in size. I define the cell border by eye. Thank you so much. --Mayfare (talk) 23:23, 21 January 2014 (UTC)

Great, thanks - I'll ask my colleague about this. It might be a few days before I get a chance to speak to him (he works in a different building), so if this question is archived by then I'll drop you a note on your talk page. Equisetum (talk | contributions) 11:56, 22 January 2014 (UTC)