EnzymeX - A plasmid editor for the mackind

While ApE is for the masses, EnzymeX is for classy Mac users. Read on for more...


4Peaks is a pretty well-known piece of program used for work with DNA sequencing trace files. EnzymeX is made by the same guys. Their website has a few other interesting programs for Mac users that are worth trying. EnzymeX is a feature-rich plasmid construct designer and editor. You can download EnzymeX from their website for free. Installation, as with most other Mac softwares, is a simple drag-and-drop of the app into 'Applications' folder.

When opened, the program comes up with three choices: creating a new construct, opening an existing construct, or looking up enzyme information. Using this program, you can design your plasmid construct in silico. If you are designing a protein expression construct, you can translate the insert to make sure the gene insert is in-frame and/or protein sequence is correct.

Going into the details of the program with a full feature list is beyond the scope of this entry. I will however highlight a few things I liked.

• The search box on the top right corner of the main window is fantastic. You can not only search for restriction enzyme sites, but also sequence and sequence motifs (DNA and protein).
  
• 'References' is a nice feature. It has a list of commonly used abbreviations, amino acid structures, codon tables of different organisms, and kozak sequences. In addition, there is a 'buffer composition' table that lists the composition of restriction enzyme buffers bundled with enzymes by different suppliers. If you end up with a sticky end DNA molecule and would like to modify it, 'References' can help you. Just tell the program what you want to do and it will tell you what to do - neat! Finally, the program also lets you visit the ReBase info webpage of any selected restriction enzyme.
  
• 'Calculator' tool is very handy when you have to quickly find out the concentration of particular sample, or convert between micrograms and picomoles, micromolar to picomoles, picomols to ends, etc. Calculator tool also tells you the molecular weight (in kDa) of a particular nucleic acid fragment based on the number of nucletoides; length, molecular weight and estimated Tm of a given oligonucleotide sequence; and given the insert and vector size and concentrations it will even help you set up a ligation reaction!
  
• With EnzymeX, setting up those double digests is very easy. Choose the enzymes and the supplier, this program will tell you which buffers to use. Reaction Mixer will even help you set up the restriction enzyme digestion and lets you print the set up - now that's convenient!
  
• EnzymeX's features are further enhanced by Plugins. I only have a few plugins. One of them allows me to instantly view the hydrophobicity of a translated region of the construct.
  

In my earlier post, I mentioned about a similar program called ApE. While ApE does most of the things EnzymeX does, it lacks the fine interface EnzymeX has. Also, ApE lacks almost all the vendor-specific restriction enzyme features EnzymeX has. I find those features very useful and I am sure anyone who uses a bunch of restriction enzymes (especially from different vendors) routinely will appreciate those features in EnzymeX. One feature that I would like to see in EnzymeX is its ability to open and align ABI chromatogram files with existing constructs (EnzymeX lets you use NCBI BLAST which includes BLAST2Seq). That feature is present in ApE and it is something that I use very frequently. Other features that would be a nice addition to this program include the ability to make nice pictures of plasmids for presentations and publications; ability to design compatible PCR primers, set up PCR reactions much like restriction enzyme digestion reactions, and visualize products in a schematic agarose gel; and ability to design mutagenesis constructs and the primers required for them. In most cases, after plasmid constructs are designed and the genes sub-cloned, attention of the researcher shifts to protein analysis. Addition of useful features for protein analysis like secondary structure prediction from PSIPRED, protein motif recognition, displaying protein parameters as in ProtParam, etc., would make this program even better. It is a pity that this program is available only for Mac users. It would be excellent to have this program available for Microsoft Windows and GNU/Linux users also (I have a MacBook, two computers running Kubuntu and I share a lot of constructs with Microsoft Windows users). I would like to congratulate Mek and Tosj for such a wonderful job creating EnzymeX and thank them for providing it for free.
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Biking in Fairhill NRMA

Fairhill is a wonderful place for biking; and very close to Newark too. We went biking here a few times earlier too. But, this is the first time we had the GPS on us.





Fairhill Natural Resources Management Area (NRMA) is located just off of Rt 273 across DE/MD state line. Parking is not free - Maryland vehicles pay $3 while out-of-state vehicles pay $4. Park maps are available for purchase at the Nature Center on Tawes Dr. Although there is a map available on the website, it is of low resolution and is not useful as a trail map. You can purchase a trail guide with maps online for $6.



We parked in the parking lot on Tawes Dr. A park map is posted near the parking lot. We wanted to get a copy of the map from Nature Center. However, it was closed on that Saturday. A park map was posted near the Nature Center too. We decided to go on the Orange Trail and started off from Nature Center. After biking on Tawes dr we entered Orange trail on the left. The idea was that we get back to the same place when we finish biking on that trail. However, we lost our way after biking about half way! At least for the first half of the trail, it was very well marked with orange blazes along the trail. Although there were a few hills to climb, the climb itself was not very difficult. Luckily though we got on the trail from the 'easy' side. I feel that it would have been a little difficult in the opposite direction. Next time, we will give that a try and write how that felt.



Here is a map of our path with a flag marking the place where we should have taken a right (instead of left) in order to be on the orange trail.





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Biking in Brandywine Creek State Park

This is a trail we biked on a little while ago. I just got around writing about it now. I do not remember a lot about it other than that we had no idea what we were doing!



We took off from the trail head at the parking lot near Thompsons Bridge Rd. Thompsons Bridge rd is just off of Route 100. Park entrance falls just beyond the bridge on Brandywine Creek. Delaware vehicles have to pay $3 for parking while out-of-state vehicles have to pay $5. There is a small office at the entrance. If it is open, you can get a copy of park map. You can also download a pdf file of the map from here.



Among others, we chose to bike on what is a part of northern delaware greenway. If you plan to take the same route, park map might not be very useful. Without a copy of park map we did not realize at that time that the path we took was not really on the map! Overall, our ride was very enjoyable. It was an 8 mile-long loop with a few serious hills to bike up, and down. The trails were not at all marked. May be the trails that are shown on the map are marked; but not this one.



This part of the park has a small picnic area next to Brandywine Creek. We saw a few people with their boats. You cannot rent a boat here though. On the other side of the path we took, there are a few hiking and/or biking trails. With opportunities for biking, hiking, and boating, this place could be a good destination for a day-long picnic.



Here is a map of our path and it's elevation profile.



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PDFs, Firefox and Mac

If you use Firefox as the primary web browser on your Mac, then you must have noticed that it is a pain to work with a bunch of PDF files. Luckily, now there is a solution.

As a part of my work, I need to open and work with a lot of pdf files. Often, these are research papers published in scientific journals. When I click on a link to open a pdf file, Firefox-Mac (unlike Safari) cannot open that pdf file in the browser window. It will download a copy of that file to the disk and then (if you have set the preferences that way), Preview.app will open it. It is really annoying because then I have to switch windows (Firefox to Preview) in order to work with a webpage and a pdf file simultaneously.

A good friend sent me a link to this post on Ars Technica that talks about a Firefox PDF Plugin for Mac. You can download that plug-in directly from this website. All you have to do is to click on 'Install Now' link to download and install this nifty plug-in (This plugin requires that you use Firefox 3. If you haven't done it already, you should download and install Firefox 3. You have to restart firefox after installation).

As good as this plugin is, it has a few important issues that need to be worked out. These are a few things I noticed:

• Go to this link to open a map of Smoky Mountain National Park from the website of NPS. First thing I noticed, the cursor is in 'text selection' mode. On a map like this, I would like to click-and-move around the map area which is not possible. Only way to move around the map is to use scrollbars.
  
• With no toolbars, it is difficult for users to know how to Zoom-in/Zoom-out. Cmd+ or Cmd- keystrokes do that job.
  
• To 'Save' this PDF file to disk, you need to go to the 'File' menu, Click on 'Save Page As...' and save it as a PDF to disk. Similarly, in order to print, you need to go to the 'File' menu and click 'Print'.
  
• Go to this link to open a scientific paper from the Journal of Biological Chemistry. This pdf file is now part of a frame in the current window. Saving this pdf file to disk following the method mentioned above does not work. Nor does the trick to print.
  [Update: You can still save the pdf from 'File' menu. Click somewhere in the pdf to activate the frame. Then uust choose 'Save Frame as...' instead of 'Save Page as...']
  

With these few issues (that I came across in the first few minutes of my usage; and a few more found here) still to be ironed out , this plugin needs to be perfected. In spite of that, this is a wonderful extension - the one that I have been waiting ever since I bought my mac. Thanks to colesbury and everyone else involved with firefox-mac-pdf plugin.
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Gnome-Do on Kubuntu

After using Quicksilver on Mac, I always wanted a similar program for linux too. I used Katapult for a while. Katapult is okay; but it has a few shortcomings.
Recently, I came across Gnome-Do.

"Inspired by Quicksilver and GNOME Launch Box", gnome-do in its most basic form lets you launch programs and files from your computer.

Installation was very easy. Just go to Adept Manager and search for gnome-do and install it. However, that was not the latest version of the program. So, I followed the directions found here to add a repository and install the latest version.

Once installed, run the program from 'Run Command...' entry in the K-Menu. Type 'gnome-do' and hit enter. I just noticed that there is an entry in K-Menu > 'Utilites' for Gnome-do. Gnome-do interface box appears on the screen. Start typing for the program you want to start and you will see the results appear in real time. Use up and down arrow keys to go through other choices. Click on the small triangle present at the top right corner to go to 'Preferences'. In the preferences pane, you can add a host of plugins that enhance the use of this little program.

All this is great, but there is at least one bug that makes this program almost unusable. When gnome-do is summoned by Super+Space keys the interface screen ends up behind the active window. If the active window is large, you cannot even see gnome-do interface screen. This bug has been reported and hopefully it will be fixed soon.

Until then, I am back to Katapult.

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Creek Rd Biking

I previously wrote about biking on Creek Rd here and here. This one is a longer version...

Start at the intersection of Lovett Ave and Academy St. There is a parking lot here. If you have a University of Delaware Parking Pass you can park here. If you do not have a parking pass, you can still use the pay-per-use spots (either in the parking lot, or on Academy St). If you are planning a day trip to the university area, consider getting a day-pass from the University of Delaware that can be used to park your vehicle in any of the University parking lots (more details here).

With a lot of parking areas through out the trail, you can start at a different place on this trail. In total, this trail is about 16 miles long. Oh, and one more thing - this is not a marked trail. I don't even know what this trail is called! Print a copy of the map below and you should be able of figure out the path very easily.


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Tri Valley Trail

Another nice day, and we are out in the woods. Middle Run area was the destination this time too.



This trail is a 7 mile long loop starting from Middle Run area parking lot. Unlike several other parking areas in White Clay Creek State Park (WCCSP), this one does not require any parking fee. For the most part of the trip, we were on one of three trails: Tri Valley trail, Whitley Farms Trail and Bryan's Field Trail.



At the trailhead, we took a right turn (towards East) to enter Lenape Cutoff Trail. Lenape Cutoff trail intersects Tri Valley Trail. All these trails are marked very well. After biking for a little while, Tri Valley trail passes through Fox Den rd. Get off the bikes and cross the road carefully to continue on Tri Valley trail. After biking some more, you will see some houses and trail enters that community. Continue on Smithmill rd and go past Papermill rd to reach WCCSP Possum Hill area parking lot. At this point, follow directions for Bryan's Field trail connector to enter Whitley Farms trail. We biked on Whitley farms trail earlier; this time we bike in the opposite direction. Continue on Whitley Farms trail and bike past WCCSP parking area near Thompson Station rd to enter Bryan's Field trail using Whitely Farms trail connector. Continue on Bryan's Field trail and look for Papermilll rd connector. Cross Papermill rd to enter Middle Run area and follow Lenape trail to return to the Middle Run area parking lot. As you can see from the elevation profile picture, there are a couple of uphill climbs - not something very difficult but it is good to keep that in mind. At the parking lot on Smithmill rd, you can take Bryan's Field trail instead of Whitley Farms trail to shorten the loop by about 3 miles. This would skip one of those uphill climbs too.



As I mentioned before, grab a copy of WCCSP map from Ken's website. It is a lot easier to visualize the trail on that map. You can also download a .kml file from the google map shown below that can be used with a GPS device.





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VirtualBox - New and Improved!

Today, I grabbed a copy of the updated version of VirtualBox. Among other few improvements, VirtualBox for Macs now includes support for Shared Folders.

VirtualBox 1.6 comes with several updated features. You can find out about them here. Of interest to Mac OS X are:

• MacOS X: fixed seamless mode
• MacOS X: better desktop integration, several look’n’feel fixes
• MacOS X: switched to Quartz2D framebuffer
• MacOS X: added support for shared folders
• MacOS X: added support for clipboard integration

Support for Shared folders is something that I missed in the earlier version. With some help from a friend who understands computers better than I could ever do, I got the shared folders feature working in the previous version too. Having that feature work out-of-box is better.

First, you need to download the latest version (1.6) from this website. Installing it is straightforward. Once, installed, it will upgrade your earlier version to the latest one (the icon for newer version changed).

When I opened the new version for the first time, it popped up a message something about my settings from the previous version. I chose to Backup those files and proceeded.

In order to get the Shared Folders feature working, follow these steps:

• Click on 'Devices' menu of the virtual machine window. Among the list of choices, choose 'Shared Folders'. A 'Shared Folders' window appears.
• Click on the small folder icon with a plus sign on the top right corner to add a new folder that you want to share between Mac and Windows. Another windows pops up.
• Browse to the folder that you would like to share by clicking the 'Browse' button (little folder icon in the top right corner). It is a good idea to choose your Mac {username} folder. Give a name to that share. Check 'Make Permanent' and then click 'OK'. You will return to the 'Shared Folders' window. You can see your shared folder appear below 'Machine Folders' list. Click 'OK' to exit.
• Now, go to 'My Computer' in WinXP and click on 'My Network Places'
• Click 'Add a Network Place' on the left hand panel. 'Add Network Place Wizard' opens. Click 'Next'
• Among the choices for 'Service Providers', select 'Choose another network location' and click 'Next'. A folder selection box appears
• Browse to 'My Network Places' >> 'Entire Network' >> 'VirtualBox Shared Folders'. Here you will find the folder that you shared earlier using 'Devices' menu in VirtualBox VM as '\\VBOXSVR\...' Choose that folder and then click 'OK' to exit. And 'Next' to continue
• Give a name to that network place. Click 'Next' to continue and then 'Finish' to end the wizard

That's it! You now have access to all your Mac files. Just go to 'My Network Places' to see your shared folder.

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Middle Run Area

A 5.3mi long loop that Sachin and Gajju biked on. It is not one particular biking trail - it is a mix of a few of them. Click on 'Read More' to see a map and elevation profile.





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Bryan's Field Trail and Whitley Farms Trail

With the days getting warmer, I am back to biking. Yesterday, we went mountain biking for the first time this season. We took two trails in White Clay Creek State Park Possum Hill area. Click on 'Read More' to see a trail map and elevation profile of Bryan's Field Trail and Whitley Farms Trail.



Bryan's Field Trail can be accessed from the parking lot of Possum Hill area (Parking is not free from March 1. Delaware vehicles pay $3, whereas out-of-state vehicles pay $5). We first took the Bryan's Field Trail. It is about 2 miles long. There is a shortcut (we did not take it) that comes after a quarter mile into the trail. Bryan's Field Trail is very well marked. In spite of that, we took a wrong turn and ended up at the intersection of Paper Mill Rd and Thompson Station Rd. - hence the off shoot on the trail map!









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After we finished our adventure on the Bryan's Field trail, we decided to bike more. Thus, we came up with another loop starting from the same parking lot and entering into Whitley Farms Trial (Whitley Farms Trail can also be accessed from another parking lot near Thompson Station Rd). This trail (which I am calling Bryans - Whitley trail here) is just over 3.5 miles and a lot more fun than Bryan's Field Trail. Starting at the the Possum Hill area parking lot, we followed Bryan's field trail for a little more than half mile when we took a right on the fork to enter Whitley farms trail. Whitley Farms trail is also very well marked. There are a few of shortcuts that can be taken to get back to the parking lot if you are feeling tired. In less than 0.5 miles after entering Whitely Farms trail from Bryan's Field trail, you come across the parking lot near Thompson Station Rd. About a mile and half later, you would intersect with Tri Valley trail. At this point, a right turn on tri valley trail will lead you to the parking lot. Last shortcut comes about a mile after the intersection with tri valley trail. At this fork, taking a right turn would lead you back to the tri valley trail where you should take a left turn to reach the parking lot. However, this is about 0.2 miles longer than the other option. We chose the shorter version - took a left turn and reached the parking lot to finish the loop.









View Larger Map



Note: Click on 'View Larger Map' to view a larger map in Google Maps. If your computer has Google Earth installed, click on 'View in Google Earth' on the Google Maps page to download a .kml file.


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White Clay Creek State Park Map

Please visit this website to find a neat map of White Clay Creek State Park.

This is an unofficial trail map designed and constantly updated by Ken. You can download a pdf file from that website. It not only shows the trails and their respective mileages, but the map also gives a rough idea of the elevation. Further, this map even lets you choose the information you want to be displayed. This map is a lot better than the official map and is more up to date. Although it is designed with bikers in mind, it is a valuable resource of information for hikers too.
This map is being constantly updated, so pay a visit every once in a while for the most up-to-date version.

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VirtualBox - Windows on Mac for free!

Virtualbox, is a virtualization software. It can be used to run Windows on Mac OS X. In that respect, it is very much like VMWare Fusion and/or Parallels. However, Fusion and Parallels are commercial software programs - you need to buy a license. Virtualbox, on the other hand, is available free of cost for download under GNU General Public License.





I came across Virtualbox a little while ago while futzing around in the internet tubes. However, at that time the virtualbox for OS X hosts was still beta2. With no real necessity for me to run Windows on Mac at that time, I decided to wait for the final version. As a part of my research, I now need to use a particular Windows program. So, before I shell out $$ for a copy of Fusion or Parallels, I decided to check up on Virtualbox.



Virtualbox for Mac OS X hosts (beta4) is now available for download here (~21MB disk image file). Once downloaded, in order to install, double click on the file to mount the image and simply drag the Vitrualbox app into the Applications folder. In order to run Windows on Mac, fire up the app and click on the 'New' button on the top left corner to create a new virtual machine. A wizard will guide you through the installation process.







Click 'Next'.





Give a name to your virtual machine. Since, I was going to install Windows, I named it so. Then, pick the 'OS Type' from the list and click 'Next' to continue.







You need to choose how much memory you would like to allocate for Windows. Whatever amount you choose here, that much amount of memory would be unavailable for other OS X apps when the virtual machine is running. If your computer is low on memory to start with, you should not allocate a lot of it to the virtual machine here. 192MB for Windows is a good bet; but I chose 512 in this particular case.







You now have to allocate hard drive space for Windows. If this is the first time you are using Virtual Box, it is very likely that you do not have a hard disk image already. So, you have to click on the 'New' button to create a new one.







A new window appears that will guide you through the steps to create a new hard drive image. Click 'Next' on the new window to continue.







There are two types of virtual disk images: one that dynamically expands and one that is of fixed size. You can pick any kind; in this case I picked one of fixed size.







A filename for your virtual disk image is automatically entered - it is same as the name of your virtual machine. For size, I allocated 10GB for Windows. If you think that you would need more space for files in your Windows partition, you should increase the size here. However, you should keep in mind that the hard drive space you allocate here would be immediately deducted from your total hard drive space on the Mac. So, if you are running short on your Mac hard drive space, you should stick to the minimum. Also, if you are not sure how much hard drive space you want to allocate for windows, go back and pick the dynamic kind of disk image. Once you are done, click 'Next' to continue.







Click 'Finish'. The setup will now start creating a virtual disk image. A little window with a progress bar will appear. It takes a few minutes to create the disk image. So, be patient.







Once the disk image is made, you would go back to the previous window - now with the boot hard drive selected.







Click 'Next' to continue and then 'Finish' to finish creating a virtual machine.







Once the virtual machine is created, you should see it in the main Virtualbox app window like this:







The default settings for a virtual machine should be okay. However, if you are a little adventurous and would like to tweak the settings of your virtual machine, you can do so by clicking the 'Settings' button.



Now, insert a Windows installation disc, select your virtual machine and hit 'Start'. You would see a new window of virtual machine and it boots from the Windows installation disc. Follow on screen directions to install Windows. Once, you are finished with installing Windows, you need to install 'Virtualbox Guest Additions'. In order to do so, Device > Install Guest Additions. Follow on screen directions to install Virtualbox guest additions. You would have to restart the virtual machine after installation.



That's it! Enjoy(?) Windows on your Mac.


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Annoying Spaces

One of the features I eagerly looked forward to in Leopard was Spaces. After using multiple desktops (also known as Workspaces) in Linux, I always missed that feature in OS X and Windows. When it was announced, I assumed that Spaces in OS X would be exactly identical to multiple desktops in Linux. That, I realize now, was a wrong assumption.

As much as I like Spaces, I feel that it is half baked and nowhere as powerful and/or useful as the multiple desktops in Linux. Here are a few annoying things I noticed:

• I use two spaces most of the time; one for work-related windows and the other for e-mail, IM, web browsing and other stuff. However, there is an overlap in the apps I use for work and personal stuff. For example, I use several web-based applications as a part of my research work and so, I use firefox for both work and personal stuff. Now, say, I open up firefox window in my 'Work' space and start doing something. After a little while when I feel like checking my e-mail and go to 'Personal' space and click on the firefox icon in the dock, I expect to see a new firefox window open up in 'Personal' space. However, that does not happen. A click on the firefox icon in the dock, whichever space I am in, will take me to 'Work' space where a firefox window is already open. Thus, I am forced to use different browsers for Work and Personal uses. This happens with each and every program (for example, Adobe Acrobat and Preview). One might say, I can open a new firefox window and use it in a different Space. Unlike with Safari, right click (or Ctrl+Click) on the Firefox icon in the dock does not give you a choice to open a new window. So, I have to open a new window of Firefox by going to the 'File' menu (or by Cmd+N) and drag it into a different space.
  

• Cmd+Tab cycles through all the 'Applications' (as opposed to 'Windows' in Linux or Windows). That is not a big issue when one has only one Space. However, when I have multiple windows of an application are open in different Spaces, it becomes an annoyance. Let me explain in a scenario: open Firefox window in Space 1 - call it Firefox window #1. Then open another Firefox window in Space 1 and drag it into Space 2 - call it Firefox Window #2 (you cannot open another Firefox window in Space 2 directly, remember?). If you use Cmd+Tab to go back to Firefox from any other program open in any Space it will by default take you to Firefox Window #1 in Space 1. In order to get back to Firefox Window #2, one has to use Cmd+~. Now, close Firefox Window #1 in Space 1. If you use Cmd+Tab to get back to Firefox from any other program, you expect to get to Firefox Window #2 in Space 2 because it is the only Firefox Window now open - right? But it does not happen. It will take you to Firefox (in Space 1) but because it cannot find Firefox Window #1 there it will just activate the Firefox application - you can see it in the menu bar and that is all. If you want to go to Firefox Window #2 you should click on 'Window' and select the Firefox Window #2 (whatever it's name is). What a pain!

• When working with, say, Firefox in Space #1 where a Finder window is also open and go to Space #2 to check something in another Finder window in Space #2; Finder window in Space #1 is activated when I get back (I expect Firefox to be active - as I left before I switched to Space #2). Exact same behavior with Safari windows too.

• [Added 12/29/07] Just noticed this; I had a few apps running in Space #1 (Finder, NeoOffice, a window of Firefox, Thunderbird and Adium to be specific) and was browsing internet (so the Firefox window was the one on top). I decided to check what is open in other Spaces. So, I started going to other Spaces using the Ctrl+arrow keys. Nothing was open in other Spaces. By the time I came back to the first Space, instead of Firefox window (which was on the top of all other windows when I left Space #1) Finder window appeared on the top! This happens even when I try it the Ctrl+[number] way. This does not happen when there are no Finder windows open in Space #1 (I return to active Firefox window only).
  

So far, these are all. The list might seem small, but the issues are important enough for me to stop using Spaces.
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Safari and Automatic Session Save

This morning I was working on some stuff in Safari with about a dozen tabs open and a popup appeared asking me if I am interested in updating Leopard. I said yes; but it popped up another message asking if I am willing to restart the computer in order to install the updates. None of the tabs open in Safari were very important; I could get back to them very quickly later. So, I decided to close all of them and let the computer install the updates (and give me a short break from work).
After restart, I fired up Safari to get back to my work. I went to 'History' to see if I can get back to where I was quickly. I discovered that Safari 3.0 automatically saves the session before quitting. Just a click on 'Reopen All Windows From Last Session' got me back to where I was! Nice.


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Creek Rd Biking - a variant

Here is a map of Creek Rd trail with some minor modifications. Instead of continuing on the Tweeds Mill Rd., you go over the bridge near Wedgeweood Rd. and bike on the other side of the creek. Immediately after crossing the bridge if you take a left you will be on a trail that runs almost parallel to Tweeds Mill Rd. (shown in map). However, if you decide to go straight after crossing the bridge, you would have climb a hill before you end up in the parking lot of some place on Paper Mill Rd.


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Creek Road Biking

Several trails - short and long - are present close to Newark, DE. This is the first among the few I intend to scribble about.

The trail starts at the junction of E. Main St. and N. College Ave. If you do not have a University of Delaware Parking Pass, you can park your vehicle in the Trabant Parking Garage on the Main St. North College Ave. becomes Creek Rd. White Clay Creek falls on to your right and you would come across cement blocks on the road, which you can cross and go further. At the intersection of Creek Rd. and Wedgewood Rd. you will find a parking lot. Creek Rd. becomes Tweeds Mill Rd. from here. You can continue on the trail along the creek. On the right of the parking lot there is a bridge that goes over the creek. If you cross the bridge, you can continue on a trail that again goes along the creek (this time the creek is on to your left). This trail will end in Hopkins Bridge Rd.

At the intersection of Tweeds Mill Rd. and Hopkins Bridge Rd., there is a White Clay Creek Nature Center. Restrooms are available the Nature Center Parking lot. If the nature center office is open, you can get a park map there. Tweeds Mill Rd. ends at the Nature Center. However, you can continue biking on the trail that starts at the nature center. Trails are marked by a blue line on the trees. On the map, this trail is marked as MD for Mason-Dixon Trail. Although the map shows a pink/blue trail loop, the trail on the right side of the loop is only for hikers. Continuing on the MD trail would lead you to the Pennsylvania White Clay Creek State Park Office at the London tract meeting house. A parking lot is present here and you can get a map of White Clay Creek State Park that falls in Pennsylvania at the park office.

All the way, the trail is flat and wide - no difficult hills to worry about. You can take your comfort/city bikes apart from mountain bikes on it. Other than the nature center at the Hopkins Bridge Rd., there is no place to get water or anything. So, you might want to carry water. Patch kit is not really necessary; but it is a good idea to carry one. With the creek adjacent to the trail almost all along, bugs can be an issue.


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Biking

For fun. For health. For earth.

I used to bike as a kid. I biked a for a couple of years during my college. But it was biking as a means of transportation during those times. After I came to the US to do my PhD, I started biking, again as a means of transportation till I bought a car. Only a few months ago, I discovered the 'fun' part of biking. And that is what all this rant is about.

My wife had an old bike which she was not using; but wanted to start using. This time around, we wanted to use the bike not just for transportation, but also as a recreational tool. Since the old bike was - um - old, we bought a new bike. I wanted to buy one too, but I also wanted to first make sure that I like biking (and I wanted to do some research into what kind of bike I want). So, I got the old bike fixed and decided to use it. One of our friends is a little into mountain biking and he suggested we go biking on a trail. When we were thinking of biking, we mostly had road biking on our minds - never thought of taking the bike into the forest and all. Anyway, on one fine weekend morning my friend, my wife and I went biking on a nearby trail in White Clay Creek State Park. We were so unprepared for the trail, that we did not even have helmets! And my old bike's handle bar was rotating 360 degrees whenever it wanted to!! Nevertheless, we had lots of fun. We did some shopping for helmets and hydration packs and our weekend agenda was pretty much set for the season - biking!

A month or so after we went on our first biking trip, my wife gifted me a new Cannondale F7 Disc mountain bike. It is an awesome set of wheels and I love it. I did some research into bike buying before I decided on the Cannondale. Several websites got me started with the types of bikes that are available. A mountain biking book borrowed from the local library helped me understand the parts of the bike - how they look; how they work and what I should look for. The best part about bikes is that all the parts are visible to the naked eye and if you spend a little time with the bike it is very easy to understand how they work. Most of all, I bugged my local bike shop people - they were very helpful in explaining me the differences in the bikes which are priced differently. If you are planning to buy a bike too then my suggestion is to go grab some biking book from your local library (preferably the one with a lot of pictures) and do some reading. One of the websites I came across that helped me a lot is Jim Langely's Website. Paying a visit to the bicycle manufacturers website is also a good idea. Performance Bike and Price Point are two online stores where I found good deals on several parts/accessories. Performance Bicycle has stores across USA. If your town happens to have one then you should check it out. You can always buy a bike online and get it shipped to the store. You would need a few accessories almost immediately after you buy a bike. A helmet is must if you intend to ride on trails. Almost all bike stores carry small bags/pouches that can be tied under the seat. I find them useful to put my keys, wallet and cellphone. If you do not have a hydration backpack, then a bottle cage and water bottle are important. If you are serious about biking, then you should consider buying a backpack with a hydration bag. It doubles up as a carrier for your other personal stuff and simple biking tools. Biking tools that one might want to carry include a patch kit and/or extra tube; a bike tool kit and a bike pump. These are the accessories that I use most and feel that fall into 'required' category. A quick look at any bike shop will reveal a host of other tools/accessories. Depending on your need, use and/or budget you can go for other accessories.

I can continue the rant; but the single most important point is to 'use the bike'. The more I bike, more I am learning about it. So, if you are even remotely interested in biking you should give it a try.
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NPR on the Road

I listen to NPR in my car. If you are like me, on long drives you often come to the point where you loose your NPR member station's signal. If you do not know the frequency of the local NPR member station, then the only choice for you is to scan through all the available frequencies - a distracting procedure.

NPR website now has this nifty feature called NPR Road Trip. Enter your Start Address and End Address, NPR will give you the dirving directions and tell you which stations you can tune into on your way!
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A Plasmid Editor

I am a biochemist. And as almost every biochemist these days, I do some sub cloning. Working with all those DNA and/or protein sequences can sometimes be confusing. I always wanted a small program that can help me organize those sequences. So, one fine day, I set out on a search for that perfect program. Some of my criteria were:

• Interoperability I use a Mac Book. My home computer runs on Linux and about a dozen computers in my lab run Windows. So, I am looking for a program that can be run on all three platforms.

• Free Plain and simple. I don't want to pay any money!

• Simple and Intuitive I do not want to spend a lot of time figuring out how to use the program. I want to get on with my work, right away.

After some googling, I found this program called ApE. ApE stands for A plasmid Editor. ApE is available for download here. It can be run on Windows/Linux/Mac. I won't go through the features; but one can pretty much do all steps of sub cloning (on the computer) using this program. It has a nice intuitive interface. Although the program comes with a .doc documentation file, I never had to even look into it to use it! The author says this would be the last release of this program; so that could be an issue. Anyhow, I like this program even in its present form - there aren't any features I feel it should have and I did not encounter any bugs.
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Aadi

What does 'Vamsi Gaadi Gola' mean? Vamsi's chatter (that's the best I could get to; telugu people can suggest better, and more interesting, translations). And the title of the post - Aadi - means 'beginning'.

That sorted out, I feel I should tell right away what this blog is about. In short, it is about anything I feel to write about! For now, I can think of things like: nifty programs that I find useful as a biochemist, my experience with linux and opensource (I prefer freeware) software in general, etc. I have no fixed plan. So, there is no theme and I can (and will) write about anything. If you are more interested in what's happening in the lives of 'the herd', you should check out the herd's blog at www.vamsiandprabha.com
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