Natural Blogarithms

I wish I’d thought of that.

Thanks to a post in LifeHacker, I have set up a few bookmarks in Firefox that will open in the sidebar. I recently discovered the trick of opening links in the sidebar but I did not think to use mobile apps such as the new iphone app in Google Reader.

Some other mobile web apps that I am likely to use include:

• Digg: http://digg.com/iphone
• Facebook: http://iphone.facebook.com
• Twitter: http://m.twitter.com
• Facebook Chat: http://www.facebook.com/presence/popout.php
• Remember the Milk: http://m.rememberthemilk.com
• Wikipedia: http://wikipedia.comoki.com/

If you want more suggestions to things to stick in your sidebar, go straight to apple for some ideas: http://www.apple.com/webapps/index_top.html

The “how to” comes from Mozilla Links

And it’s pretty simple:

1. Open the Bookmarks Manager (Bookmarks/Organize Bookmarks…)
2. In Firefox 2, in the File menu, select New bookmark… In Firefox 3, press Organize in the toolbar and select New bookmark…
3. Enter a name, http://www.google.com/reader/i/ for location, and ensure to check Load this bookmark in the sidebar.
4. Press Save Changes and now you can select the bookmark to load Google Reader in the sidebar.

Try it out. It’s handy.

written by SplineGuy

As a Microsoft fanboy, I have to point out a recent result from a contest at a security conference.  It was a three day contest where hackers were challenged to access a file on variety of systems including Microsoft Vista, Mac OSX Leopard, and Ubuntu Linux.  Winners could win a  Sony Vaio, Fujitsu U810 and the MacBook as prizes. 

On the first day, the system was loaded the operating system alone and all three stood the test against the hackers and the file remained inaccessible. 

On the second day, software that is typically packaged with the operating system was included on the systems.  The first machine fell.  And no, it wasn’t Vista.  Vista and Ubuntu survived the second day, but it was the Mac that was hacked through an undisclosed (but probably widely know) security flaw in the Safari browser (in under two minutes, by the way). 

On the last day where third party applications were installed on a new patched system, a vulnerability in Flash was utilized to compromise Vista. Ubuntu was left standing alone at the end of the contest.

TechBlog: Mac hacked, pwned and owned at security conference

written by SplineGuy

They’re getting more sophisticated.  I’ll be keeping a closer eye on my students.

HT: ISTP Dad

written by SplineGuy

Okay, I confess upfront to being a Google fanboy. How can I not be when they get so many things right.

Here’s one more thing I just discovered that has made my day:

Google Reader

I use Google Reader to keep track of all the blogs that I read on a regular basis. I have a number of tags ranging from bioinformatics to edublogs to math and science. My most populated category is my Personal tag which has blogs of friends and even the facebook status updates. I was just complaining the other day that I don’t really ever see what is going on at a persons actual site. The way that Google Reader works (and just about any RSS feed reader works) is that it periodically checks a particular feed (which is just a text file in xml format). If there is new data, say a new entry, it is downloaded into the reader and I can go through a read all new blog entries.

There are two problems with this system that I wanted a nice, elegant solution to. The first is that I never actually see the blogger’s page because only the content is downloaded. Some pictures are download and some embedded videos will play but not always. Plus I’d like to see the design of the sign. It helps me to associate with the blogger who I am reading. In any reader, you can click on the name of the blog entry or even the title of the blog and visit their website directly. But this is a hassle because then you have to go back and forth between the blog and the reader. I’m kind of a one track mind so I often get lost.

In comes the Google Reader goodies. Under Google Reader, you can go into Settings and click Goodies. I have been using a bookmarklet to subscribe to new blogs. I just discovered a new bookmarklet that I can place on my toolbar called “Next>>”. When clicked this will take you to the next unread blog at the original site. No going back and forth. You can even customize using different links for different tags. So I could have a “Next>>” for my bioinformatics tag and a separate one for my personal tag. Each time it just takes me to the next unread entry in the feed.

Google Docs

I’m trying out Google Docs as a method for posting to my blog. If this is all screwy, it is because this is my first attempt. See here for more details: Publishing Google docs to your blog.

written by SplineGuy

I have elected to attend the International Conference on Technology in Collegiate Mathematics (ICTCM) this year.  It will be my first time attending this conference. It takes place in San Antonio this coming weekend and I am really looking forward to it.  I’ll be gone from Thursday, March 6 through Sunday, March 9.

ICTCM is for anyone interested in or already using technology to teach mathematics. Helpful hands-on workshops for those beginners as well as those who are experienced with technology. There are sessions on getting started, teaching with technology in the classroom, and using technology to enhance instructors’ lives beyond the classroom.

Anyone who knows any thing about me knows that this sounds exactly like my kind of conference.  I had intended to submit an abstract and present but there was a scheduling conflict around the deadline for submission.  Shortly after it was too late to submit a proposal, the conflict was resolved.  I decided that the conference itself would be worth my time even if I didn’t have the chance to present.  Instead, I’ll spend all my time either sponging ideas off other educators or heckling them from the audience (haha).

Because Wayland only offers a mere $600 for travel and conferences, I’ve elected to stay off site for this conference.  The actual conference hotel would cost me 180 a night and so I am going to drive in from an Econo Lodge down the road which will cost me about 185 for the whole three nights.

I also have hopes to meet a few of the fellow math bloggers that I read regularly.  I hope that making contact might light a fire under me to keep my own blog better updated.  If I can fit it in, I’ll make an effort to blog the highlights as the conference progresses.

written by SplineGuy

I’m going to post a few things here that the vast majority, if not entirety, of the readers of this blog will not care about.  Nevertheless, one the reasons I post to this thing is to document my adventures in technology.  As I often say to people when giving them computer advice or programming, I know enough to know what should be able to be done "under the hood" of your CPU but in most cases I don’t know exactly how to do it.  That’s where my buddy, my pal, Google steps in.  After all, I am a confirmed "Google Master" with mad orienteering skills.

Problem:  WiFi on my HTC (Cingular) 8125 phone stopped working.  When you enter the Comm Manager and attempted to activate the wireless, the "I’m thinking" icon would spin away for about 15 seconds and then the Wifi would remain disabled. 

Attempts at solving the problem:

1. A number of soft resets were attempted, to no avail.
2. Not recalling how to perform a hard reset, I attempted to remove the battery and plug it back in.  This is when I discovered a new problem: The battery panel would not come off.  Tugging, pulling, prying. It wouldn’t budge.  I managed at one point to get my thumbnail under the plastic edge, slicing through the skin connecting my nail to my thumb.  Finally, loosening the edge and peeling it back, it was free.  Some of the label of the batter had turned up and adhered to the back of the battery panel.  All that for nothing, because removing the battery did nothing.
3. Under Settings, Clear Storage is an option to do a full reset of the phone, which I did.  This still did not help.

What to do, what to do?  Off to Google:

1. I found one forum entry describing exactly my situation (http://www.htcwizardweb.net/node/2213) but there was not solution and in fact, the author decided he was ready to buy a new phone after several respondents were unable to help:
   POSTED BY ahniedc

I had for a few months, my wifi up and running, and was able to connect to my home airport. one day, wifi disappeared. i go to comm manager and choose wifi, get the spinning circle, but it won’t turn on.

ROM version 2.25.11.1 WWE
ROM date 5/11/06
Radio version 02.25.11
Protocol version 4.1.13.12
ExtROM version 2.25.11.102
Windows Mobile 5, 5.1.195, build 14928.2.2.0

Even going to Wifi Settings from comm manager doesn’t let me do a thing, and setting up my connections, can’t see wifi.

I’ve done several soft resets, and with no luck, did a hard reset. I can activesynch to my exchange via GPRS fine.

Also, have a 1 GB mini SD card, and phone won’t recognize its there. are the two related? is my phone end of life?

2. I recalled using a registry editor to modify settings to disable GPRS permanently, since I had no use for it and it wouldn’t turn off with just software.  I figured there might be a setting I could use to bring the wifi back to life.  Alas, I got lucky and, this time, with no help from the web, I managed to get the wifi back up and working.

FINAL SOLUTION:
DISCLAIMER: I take no responsibility for any "mess" created if someone uses the following steps to fix a similar problem. Anyway, this worked for me.

• Download and run Mobile Registry Editor (make sure your phone is connected)
• Navigate to HKEY_LOCAL_MACHINE/Comm/TNETWLN1/Parms/
• Change the DWord values for the following items all to 1:
• HTCResumeWifiAfterReset
• HTCPreloadWifi
• HTCPreloadStatus
  (I’ll be honest, I don’t know which one fixed my problem but I’m not about to undo them now, in fear of breaking it again)
• Ouila! 

NOTE: I also went back and disable GPRS as before.  Navigate to HKEY_LOCAL_MACHINE/Comm/ConnMgr/Providers/{7C4B7A38-5FF7-4bc1-80F6-5DA7870BB1AA}/Connections.  On both Cingular GPRS and My ISP GPRS, change Enabled to 0.

All I can say is WOOHOO!! (and my thumb still hurts)

written by SplineGuy

I posted the following to a post-doc group page and thought it might be useful to be duplicated here:

RSS feeds provide a significant resource in keeping track of regularly updated information on the web. Most commonly, RSS feeds are used as a way of “subscribing” to news sources and blogs. Any time you see the RSS logo (orange box with radar or radio signal inside) , you have a site that can be subscribed to.

Basically, an RSS feed is just a website that is regularly updated by the content provider. It’s standard format is XML. As a user, you choose a particular “feed-reeder” to subscribe to these feeds. These can be local software clients, such as Outlook or Thunderbird. They can also be online like a webmail client. The most popular online feed readers are Google Reader and Bloglines.

Once you have decided on one of these you simply begin subscribing through that client. That can mean copy and pasting the link to the RSS feed (e.g., right click on the rss logo to copy link). Also, current browsers such as Firefox and IE7 provide an icon on or near the address bar that you can click to subscribe.

The reason I brought all this up was to suggest that RSS feeds might be used to subscribe to job postings. I haven’t checked out the sites that were brought up at the meeting, but as an example you can go to NatureJobs and perform a search. On the search results pages, one of the options in the menu to the left is “Search Results RSS Feed”. This is a custom designed link that you can use to subscribe to this search. Anytime new postings fit your search they will appear on this feed and will show up in your feed reader, once subscribed. On these other sites you might look around for the RSS logo on search results pages as this is becoming more common.

I hope this provides some helpful information. Feel free to ask some questions if you are interested in knowing more.

UPDATE: I should also mention that there are ways to create a feed on pages that don’t offer feeds for their content. The technique is called HTML scraping. If anyone is interested, I can post some details. The reason I mention this is that I noticed that the job search sites listed in our group do not offer RSS feeds for their search results and I wanted you all to know that there are ways around this. (e.g., FeedYes)

written by SplineGuy

(the blog’s not dead)

I had an unexpectedly arduous task today, actually two. They seemed relatively simple, but as most things that involve Adobe software, it was far from simple.

Task 1: Find a scanned copy of a book chapter that someone in the lab had prepared and send that back to my boss. This was challenging considered that previous members of the lab have left and there is not organized central repository of data produced by those individuals.

REAL Task 1: When found there were individual PDF files for each page. My goal: Merge PDF files. How hard should that be? Answer: If you have Adobe Acrobat (not just the reader), real easy. Other wise, I failed miserably. I tried a couple of things that I scrounged up from Google searches:

PDFCreator: I think this would work just fine, even if the interface and documentation leaves you guessing as to how you are supposed to use this software. I was able to add all my pdf’s in and then highlight them all and click “Combine”. After outputting the pdf file I realized that the original pdfs had been scanned in landscape (11 x 8.5). When combined, they all were squeezed into a profile layout (8.5 x 11), not rotated, but squeezed. After a long while of trying to figure this out, I decided to abandon PDFCreator for this exercise. I even uninstalled it since I have CutePDF for all my PDF creating needs.

pdftk: I downloaded this only to realize that while it seems like a pretty powerful and nifty tool, it was command line based and I was in a bit of a hurry. I may come back and learn to use this one but for now I had to move on.

Eventually, I found a machine with Adobe Acrobat Professional and in less than 5 minutes I had the merged files I wanted. There was in my search a freeware tool called MergePDF, but it was for Mac’s only and I don’t speak Mac.

Task 2: Fill in a form that is only available in PDF. It is not a nice PDF form where you can click on a form element and just type in. Nope, this is just your standard static pdf document. Are there any good free PDF annotators? I have used pdfAnnotator but it has a 30-day free trial. After that, it watermarks your documents if you output it in any way.

FoxitReader, which is my preferred tool for reading pdf files, has the ability to annotate, adding text to the pdf but as soon as you save it, there is an automatic header added to your pages saying it was modified by FoxIt. I couldn’t have that for this form.

I finally just used the typewriter function in Adobe Acrobat Professional but there was a new challenge: Adding a signature to an pdf file before emailing the form back.

My first option was to print, sign, scan, email. Second option would be to have an image of the signature (which I do) and paste it onto the pdf. Guess what? You can’t paste an image on to a pdf file in Adobe Acrobat. You are supposed to go back to the original editor and do it there, at least that’s what I could find out from the documentation. However, you can copy and paste an object from another PDF in Acrobat.

So here’s what you do if you want to paste an image into a pdf. This is also nice because you can preserve transparency in the image if you do this:

1. Use Photoshop to save the image as a PDF.
2. Open the PDF you just saved in Acrobat and select the image you want to copy.
3. Hit control-C or just click Copy from one of menu options.
4. Open up the destination PDF and paste away.

There was one problem I didn’t have time to worry about solving the right way. You can’t resize the image you paste. I just made sure that the original image was the size I wanted it in the original source file.

Whew! Done!

Did you ever notice that the more urgent you need something done, the harder it is to get it finished? Did I make these two issues far to hard on myself? Probably, but the problems were eventually solved and now my solution is documented for future reference. And if anybody happens to comment, I might even have better solutions next time around

written by SplineGuy

One of the broadest definitions of bioinformatics that I have come across was in Sorin Draghici’s book, Data Analysis Tools for DNA MicroArrays.

Def: Bioinformatics is the science of refining biological information into biological knowledge using computers.

Under the heading of bioinformatics is a wide variety of different fields of study with a lot of problems under its umbrella. Some of the primary issues addressed, historically, have been sequence analysis, protein structure prediction and the dynamic modeling of complex biosystems. Other areas of fairly recent research has been in protein-protein interations, protein-DNA interactions, enzymatic and biochemical pathways, population-scale sequence data, large-scale gene expression data and ecological and environmental data.

That’s what Draghici has to say about it, anyways. As a newbie, I am discovering all the time new avenues of research and trying to assimilate and categorize all the new information I’m coming across. So far, it looks like my research will begin in the areas of sequence analysis, modeling of biosystems, pathway analysis and analysis of gene expression data.

The first project in which I am involved is simply cross-species comparison of genes that have been identified in one species through expression analysis as having a role in cell wall development. We’ll use this information to predict their role in other plants as well.

I’m already having quite a good time at my new job taking care of some techie stuff, more so than I ever had a chance to do in my last profession. I’ve tweaked a website design to meet the boss’ requirements, migrated a database website from one server to another one (learning a good deal about MS SQL Server in the process), identified and solved a particular issue with the Genespring workgroup server.

I’m also utilizing a new software tool on my own server, something called activeCollab, a project management utility. It is an online database of my current projects and activities. Through a fairly easy to use web interface I am able to enter all my projects along their tasks, messages, milestones, etc. I’ve provided access to my colleagues and my PI to allow them to keep tabs on my progress. Plus, it helps me to make sure that I am staying on task and meeting all my own goals.

written by SplineGuy

When a software need arises, I have pretty standard (and probably unwise) approach to solving the problem.  Within the last couple of days, the warning popped on my work desktop that told me I was running low on hard drive space.  I am unfortunate enough to have a desktop with mere 40GB of space.  There was a day and time when that last sentence would’ve been utterly ridiculous. Anyways, my procedure is to start with a Google search to try to determine just what the best key words for my problem might be.  Eventually I narrow down on the term and go hunting at places I trust for their recommendations.  A lot of blogs (largely, TechTV alums) are my first targets.  If that fails, I move on to places like download.com or Tucows and start trying software until I find the one I like. Install, Do I like? No? Uninstall. Repeat.

I wanted to find a utility that would map out the size of my directories, so I can determine where the “space hogs” are. In some cases, I’d be able to delete large unnecessary files and in other cases, I’d move them to a larger external hard drive or network drive.

I started with a Google search for “directory size” and realized that was a pretty good start. I found nothing on my chosen blogs so I went to Tucows and found this one that I REALLY like.  I thought I’d recommend it to everyone.

:: JDiskReport ::JDiskReport enables you to understand how much space the files and directories consume on your disk drives, and it helps you find obsolete files and folders.

The tool analyses your disk drives and collects several statistics which you can view as overview charts and details tables.

This is ad-free uncrippled no-charge binary multi-platform software that never expires.

Powered by ScribeFire.

written by SplineGuy