Biochem Blogs

Biochemistry blog, science writing

Introducing WolfPub – A publication management system for webpage development

WolfPubWe are pleased to announce the launch of WolfPub, an easy and secure way to manage your publications. WolfPub is a web-based system that allows you to maintain and store your publications, then WolfPub uses the database to format and post your publications to your webpage. As a faculty member, you can create an account and then start adding your new publications in a simple and secure way. You will no longer be required to open your webpages and edit them manually whenever you have a new publication in press. Just add the manuscript to the list of publications in your WolfPub account, and the WolfPub widget will take care of the rest.

WolfPub works with PubMed and it’s own database to manage your publications. On your webpage, it formats and displays your manuscripts that are “published” as well as manuscripts that are “in press,” if any. Users are only required to add publications that are in press in their WolfPub account. WolfPub automatically retrieves your “published” manuscripts from PubMed. WolfPub also updates the database when the in press manuscript lists on PubMed. During this process, if a publication added into the WolfPub database as “in press” has been listed on PubMed, your publication will be marked as “published.” The information displayed on your webpage will then be changed accordingly to reflect the journal volume and page numbers. Because of this feature, you are no longer required to keep watching your publications for a change in status.

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Computer security is important

swartzEarlier this week the X-ray generator control computer was hacked into from an IP address assigned by an internet provider in Shanghai China.  The attack started with repeated root login attempts starting sometime before 3:00 Sunday morning and continued until success Monday morning at about 8:00 AM.

The intruders did no damage to the files on the computer but did install some software of their own which was designed to attempt to break into other computers. CALS (College of Agriculture and Life Sciences) IT discovered the break-in through monitoring suspicious network traffic outgoing from the computer and disconnected it from the network at about 9:00 AM Monday.

In recent times, there have been numerous news reports of high profile computer break-ins against large companies and other organizations.  It is not uncommon for those break-ins to be achieved using university computer facilities that are first hacked. The strategy makes it easier for hacking since activity sourced to American computers is less suspicious and it provides the hacker some insulation from discovery.

In summation, our computers are targets and we must do what we can to minimize risk.  Make sure that your fire-walls are up to date and turned on. Make sure that all of your accounts are pass-worded and that the passwords are at least 8 characters long with numbers, capitals and special characters. If you are running a computer with Linux OS make sure that remote root login is prohibited and that local root login is prohibited.

I spent the day with Patrick Stewart

christie cade

Christie Cade I'm on ScienceSeeker-Microscope

I spent the day with Patrick Stewart.  Not the actor, though both are from England. Patrick Shaw Stewart, to be more specific. He’s one of the founders of Douglas Instruments Ltd. and was here to show us the Oryx, a robot designed for automation of microseeding in crystallography. I had never done microseeding before, much less with a robot, so it was really exciting to experience.

In crystallography you have a tray which has several wells in it. In the bottom of these wells is a reservoir solution which contains a precipitant. In a hanging drop experiment, the wells are sealed by glass cover-slips (such as those for microscope slides), and a protein drop hangs from the bottom of the cover-slip. In a sitting drop experiment, the protein drop sits on a pedestal in the well, and the well is sealed with packaging tape or something similar. In both cases, the protein drop contains protein mixed with a small amount of reservoir solution, which causes the drop to have a lower concentration of precipitant than the reservoir solution in the bottom of the well. Water slowly leaves the protein drop to try to equalize the concentrations of precipitant in the bottom of the well and in the drop. Eventually protein crystals form in the drop. These crystals can diffract x-rays and the diffraction pattern can allow us to solve a structure of the protein. Check out Peter Nollert’s excellent blog on protein crystallography for more information.

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Learning to speak IT

Clay Clark

Clay Clark – @biochemprofI'm on ScienceSeeker-Microscope


Recently one of our faculty contacted the IT department to inquire about how OIT (office of information technology) charges for network connections. OIT provides web services for the department, and we’re trying to understand how data and phone services are charged. Our assumption was that the more IP addresses used, the higher the charge. The response to our inquiry is below:

[Name redacted] got in touch with me and mentioned you were interested in how the rate for data network works.  The specific formula for allocating data networking expenses is based on salary expenditures [several accounts mentioned] within a unit. As each unit tends to utilize different methodologies for sharing the expense within the unit, we have generated a spreadsheet for each OUC (2-digit) showing the specifics of how the charge was derived accordingly to the following formula:

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Apps for the academic: Checking in with the iPad

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

I’ve had my iPad2 for about a year, and I find myself using it more and more for work-related activities as I try to move to a more “paperless” existence. Based on a discussion recently on Twitter, I thought that it might be useful for my students (and others) to see a list of apps that I use the most, and why. I’m a scientist and an educator, so I tend to use apps that I find useful for my work. I note that I don’t use the iPad much for games, and when I do, the games tend to be solitaire or the like. So, if you are looking for iPad games, I suggest you look here or here. I also note that I don’t have an iPhone, so my apps are not optimized for use with both devices.

This list is divided into four categories: Productivity, Protein Visualization, Social Media/Others, and Miscellaneous. Apps that I use on a daily basis are denoted by an asterisk (*). As you may note in the descriptions, the list is a work in progress, so please leave comments and let me know how you use your iPad (or other device) at work.

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“Watch” lysozyme chopping bacterial cell wall


When nano first met biology


Using biological molecules in nanotechnology

by Xun Lu

Lysozyme is an enzyme that helps to protect us from getting bacterial infections because it can degrade and utilize the sugars in the bacterial cell wall. A good source of  lysozyme is human tears.

A single lysozyme molecule is so small that one can’t really see it with the naked eye or even under the most powerful microscope. However, scientists at UC Irvine now can use an electronic chip to record the dynamic motions of a lysozyme molecule hydrolyzing its favorite substrate in REAL TIME. It’s like using an iPod to monitor your pace during a workout except that the iPod only gives you an average rate. In contrast, this electronic chip shows the pace of a lysozyme molecule every 10 micro-seconds throughout its entire workout. Just as we hold the iPod to monitor our pace, the lysozyme molecule has to stick to the electronic chip so that its pace can be measured.

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