LabStrider for XP, Linux
preload
May 03

Mouse colony Database module released! It will be part of LabHome project,  right now, it is fully function as a stand alone program.

Mouse Colony Management Software

It is aimed to help molecular biology and genetics laboratory to keep track of their mice. It is developed in a mouse genetics lab and get tons of feed back from those people actually use it to maintain their mouse colonies.

Download: http://sourceforge.net/projects/labhome/files/labhome/alpha/StandAlone_04_30_2011.mdb/download

System requirement:

Windows XP and above
Microsoft Office 2007 and above

This is stand alone version, which means all your data is stored in this file. It is modified from a SQL Server version which store all data in a server. SQL server version is faster, stable, hold more data and center all your data in one server. However, installation and configuration of SQL server version may be challenging. Therefore, before we develop a fully automated installation program for SQL server (or MYSQL) version, we release the stand alone version first.

Initialize the Database

There are some table you need add data manually to initialize the database.
1. Building Table
Add Building name, usually the name of the building you keep the mice, can be any names.
Add Room Name, usually is the room number, sometimes it is useful to know which room the mice located

2 Mouse People
Add all the information for people working in the lab, if everyone use different database file,
just add the user of that database file will be good enough.
You have to add room number for each people. Or the program will have error message.

3.Mouse strains
You can add all the mouse strain information here.
the database get the mouse strain information from this table.
if you don’t have any strain information here, there will be no strain option when you change mice information.

4. PCR_Mark
You need add all mice marker information here so that the genotype system will work.
For p53-/- mice, genotype is p53KO-/-, p53KO is the marker, score is -/-
For p53ER/- mice, genotype is p53ERm/-, p53ER is the marker, score is m/- or ER/-

Get started

a. Start with add outsource mice to add mice that you get from other people.
b. then setup matting cage using the outsource mice as parent.
c. then view the matting cage by the cage id, add new litter, make sure you record dead mice number,
it might be useful in the future.
d. use view litter or cage infor to change the sex of the mice
e. use view litter to change mice genotype.
f. you can print cage card, make sure you set the paper to index card size, and use index card as paper.
g. Do not add record directly to the table besides those mentioned in initialization section.

Send email to yizhou.he@gmail.com if you run into problems.

If you like our program, please donate! It certainly motivates us to spend more time to make the program user friendly and easier to use.

May 01
Lab Home is a program package that is intergated together so that it is extreamly easy for PI to change to content of their lab website. You have new paper published or you have student graduated or postdoc find a facuty job that you want to update on your website, but as we all know, write html webpage and ftp upload to server is a painful process for biologist because our training is basically incompatable with computer systems.
Want a homepage for your lab to attract more innocent new graduate student and postdocs? Build website is too difficult for your? Sure, you can hire and computer tech to do it, or you can use that part of grant money to buy a computer for everybody in your lab and do it yourselves. All you need to know is some computer basics.
Lab Home choose wordpress as backbone of the website simply because user can just login to the website and change the content on the webpage. It is as easy as using Microsoft Word if it is not easier. We also choose apache friends XAMPP as server end because their installation are extreamly easy, and all the powerful system are combined and can be presetuped for you.

Default password for admin is labhome for labhome 0.1, please change the password to whatever you wanted to be. However, this password will not working for this website for security reasons, but feel free to register an account and add some post to get some feeling how easy it is to edit lab home contents.

Release note 0.1.0
—————————————

1. apache mysql filzilla packaging kit XAMPP upgrade to 1.7.3
2. Website engine WordPress upgrade to 2.9.2.
3. Default theme for WordPress changed to Carrington Blog 2.2 by Crowd Favorite
4. The following plugins installed by default:
Avatars Version 7.5 | By Peter Sterling
Calendar Press Version 0.1.0 | By GrandSlambert
Editor Extender Version 0.1 | By Benjamin Sterling
Galleria WP Version 1.2.5 | By Y2 (Yokoyama Yasuaki)
NextGEN Gallery Version 1.5.3 | By Alex Rabe
Photo Galleria Version 0.2.8 | By Thad Allender
TinyMCE Advanced Version 3.2.7 | By Andrew Ozz
WordPress Wiki Version 0.8 | By Instinct Entertainment
WP-Print Version 2.50 | By Lester ‘GaMerZ’ Chan
WP Forum Server Version 1.4 | By VastHTML
5. Refbase 0.9.5 was used and intergrated with additional function to search and import from NCBI that is not available from orginal refbase.
6. Installation guide was added.
This release may be a little buggy, but it should do it’s job, you can use it as lab website. This functional version is still for demostration perpose only althought it is a pretty good website already. The later version will not be able to upgrade from this version, so be prepared to redo all these setting later. Try this product at your own risk because I will take no responsibility for any kind of data lost. I’m sure your are somewhat prepared for this because this product is totally free of charge for acadamic use.
Sorry for my bad English,
Yizhou Joseph He
Oct 28

ApE, which is free, a great replacement for DNA Strider, and cross-platform.

Check it out : http://www.biology.utah.edu/jorgensen/wayned/ape/

It is clickable from one Window to another, multi-criterion Enzyme choice, colored, … you name it. It just doesn’t help you to find a cloning strategy, but who cares ?

  • Runs in Windows (tested on 98, XP, NT), OS X(10.3, 10.4 and 10.5), and Linux/Unix
  • Highlights restriction sites in the editing window
  • Accurately reflects Dam/Dcm blocking of enzyme sites
  • Highlights text using pre-defined and custom feature libraries
  • Shows translation, Tm, %GC, ORF of selected DNA in real-time
  • Reads DNA Strider, Fasta, Genbank and EMBL files
  • Saves files as DNA Strider-compatible or Genbank file format
  • Highlights and draws graphic maps using feature annotations from genbank and embl files
  • Directly BLASTs selected sequence at NCBI or wormbase

    Thanks for the information provided by Dr.Guillaume Stahl.

    Have fun.

    Yizhou Joseph He

    Sep 13

    I will pause the update for DNA Strider. I will focus on the development of LabHome project and change DNAStrider as client of LabHome server called LabStrider.

    The new LabStrider will be very similar as this project, except use database to store plasmid information. It will be able to connect to LabHome server and share plasmid information through the server.  Since I don’t have mac and this project receive $0.00 donation. LabStrider will not release mac version. (I move from UNC to NCI, so I have no access to intel based mac anymore). Mac user please get mac version DNA strider from Dr. Marck  christian.marck@cea.fr

    Yizhou Joseph He

    Apr 28

    I recently get response from Dr. Dennis J. Templeton that the original DNA Strider develope by Dr. Marck is updated to MacOSX (1.4f6). Therefore, there is no need for my DNAStrider project to go on. And it is not appropriate for us to continue use DNAStrider and the icon for our project. I will pause the update untill there is further need. I will focus on the development of LabHome project and may change DNAStrider as client of LabHome server.

    For DNA Strider lovers, you can obtain the OSX version of DNA Strider from Dr. Marck. This is Dr. Marck’s address, from a 2008 publication:

    christian.marck@cea.fr

    It may cost about $200 or so according to Dr. Dennis J. Templeton. There is no website for DNA Strider, so please send Dr. Marck an email.

    Thank you all for your support. Please leave you comments and thoughts on our website or send me an email at

    yizhou@med.unc.edu

    Yizhou Joseph He

    Apr 14

    DNAStrider Data Server LabHome is designed to store plasmid sequence information in centrolized server so that lab user running DNAStrider for windows XP, Linux or MacOSX can open, store and share plasmid sequence information easyly.

    LabHome is also a homepage for labortory. It is easy to install and easy to use online editing homepage system and have great potential to expand to an platform for lab manager system.

    DNAStrider 1.60 plan to support open and save plasmid information in LabHome Server.

    Please visit http://labhome.sourceforge.net/wordpress/ for demo

    http://sourceforge.net/projects/labhome/ for download.

    Apr 02

    1. Add support for restriction map.
    2. Add support for restriction map print.
    3. Add link to DNAStrider wiki.
    4. Bug fix solved the version number didn’t show up in about box.
    5. Bug fix solved the inconvince when click on restriction graphic
    6. Correct spelling mistake for reverse,complenment, calculator.
    7. Change menu item “Restriction Map” to “Print Restriction Map” and move to file menu
    8. Change Menu item “print” to “Print Restriction Graphic” under File menu.
    9. Bug fix and improved Print Restriction Graphic function.
    10. Removed the requirement for addition of “.SEQ” after the Classic DNAStrider files. But Addition of “.SEQ” is still recommended.

    Recommended to updrade.

    Mar 28

    1. Add support for restriction map.

    2. Add support for restriction map print.

    3. Add link to DNAStrider wiki.

    4. Bug fix solved the version number didn’t show up in about box.

    5. Bug fix solved the inconvince when click on restriction graphic

    Mar 21

    Finally get my hand on a macbook pro. The new release is based on windows version 1.58 and add support for .ab1 file format. 

    1. fixed the bug that close file and close all do not work as it should have.

    2. fixed the bug that different file format don’t have different icon. Add support for double click the file and open with DNAStrider. You may need to choose application and check “alway open with” and then select the DNAStrider program.

    3. All three  application for Intel, PPC,  and Universal is packed in one package, just select the right one to use.

    4. whatever change is made in 1.58. Mac user skipped 1.58.0, so this release combined the change made in 1.58.0.

    Mar 17

    DNAStrider is now released. Currently windows verion only. Linux version will be out soon. Mac version will take a while until I can borrow a macbook pro.

    VectorNTI is ending its Academic license program, but don’t panic, with DNAStrider1.58, you can use DEMO version of VectorNTI just fine. New function will come out soon to get your DNA sequence out of the VectorNTI database and convert it to VectorNTI sequence that works in DEMO mode.

    Change log:

    1. Add Support for import VectorNTI archive .ma4 format. Multiple sequence in one archive is supported.
    2. Add Support for import GeneBank .gb format.
    3. Add sequence search function.
    4. Bug fix for reverse and complementry function window open issues.
    5. Bug fix for multiple document handle issues.
    6. Bug fix for sequence scroll bar scroll issues.
    7. Bug fix for Restriction Graphic refresh issues.
    8. Add support for select sequence by click on Restriction Graphic.

    Mar 15

    The old linux file named as DNAStrider_Linux1.57 that “Realbasic for Lepard” compiles automatically will not work for sure. The newly updated DNAStrider 1.57.1_Linux.zip should works on OpenSUSE 11.1 KDE4 and Ubuntu 8.10 Desktop. The Zip file included binary file, source code, database file, sample pcDNA3.SEQ file.

    For Linux users, the extention name are case senstive. So add .SEQ to the end of classic DNAStrider files.

    If the program does not run after extract from the zip file, right click on DNAStrider program file and choose property. Then under Permission tag, check allow the execute the program.

    Mar 13

    I don’t have mac yet. The current development is on PC. Realbasic program runs a little differently between PC and Mac, so every time I need to borrow a mac for a few hours to modify and compile the program.

    Different Mac also support program differently. The mac that I can borrow runs Lepard 10.5.2 intel. So I really have no control of the quailty the program runs on other platforms.

    The Donation money will be used to buy a mac for development and test. Please note the mac model you would like me to buy. I will make decision based on the vote.

    Support This Project

    Mar 13

    1.  Add function for reverse and complementary.

    2.  Add function for restriction summary order by number of cut, the old function was renamed to restriction summary order by enzyme name.

    3.  Support for multi-document open at the same time.

    4.  Now use open to import dnastrider classic file. Make sure you add “.SEQ” at the end of your old DNA Strider file name so that DNA strider can reconize it as classic file format.

    5.  Add support for fasta format.

    6.  Bug fix.

    Feb 23

    Mac upgraded to OSX, Lepard which do not support os9 anymore.

    This project is build to help DNA Strider user to get their data out and perform some basic DNA analyze function.

    This program is still in early step of development,  I release it now only because it can read out the old DNA Strider file correctly so that people can copy and paste to other programs.

    Right now, I would recommend VectorNTI for OSX.

    Please be very careful before use any other function for now.

    You are welcome to test if these function do what it supposed to do and let me know if there is problems.