BioPythonGUI

README updated

2008-10-21T08:01:00.000-07:00

README of BioGUI has beed updated.
Add the instruction of installation on Windows.

Rename BioPythonGUI to BioGUI

2008-10-12T01:38:00.000-07:00

Peter (one of the main developers of BioPython) suggested that users may not care whether BioPython was used and BioPythonGUI should have a more generic name.

Thanks Peter's kindly advice, I decide to rename BioPythonGUI to BioGUI.

I would also thanks Anders, who give me a advice to make this project on code.google.com.

Ths following are the new BioGUI site:
Project sites: http://code.google.com/p/biogui/
Download: http://code.google.com/p/biogui/downloads/list
Blog: http://biogui.blogspot.com/ and http://biopythongui.blogspot.com/

BlastParserGUI 0.1 Released

2008-10-12T00:48:00.000-07:00

NCBI BLAST is one of the most highly used bioinformatics tools. Researches use this tool to search their sequence to the database for homology sequences. Though the parser for Blast report in bioperl or biopython has been developed many years, the parser is not easy to use for researchers except the programmers. BlastParserGUI is a nice GUI Blast report parser which use the BioPython NCBIXML module as the code level parser. It's easy to use. However, you should know that this release may have many bugs. But it will get better if you send me some comments.

Screenshots: http://picasaweb.google.com/quwubin/BioGUI#5256173967259579922
Download: http://code.google.com/p/biogui/downloads/list

BioPythonGUI: Now can run on both Linux and WindowsXP

2008-09-21T08:54:00.000-07:00

Over the past few days, I was busy preparing a paper. So I did not have much time to write code. Today, I think I should do some test on BioPythonGUI and make it platform-independently. Luckily, BioPythonGUI runs on WindowsXP without much modification. I also updated SeqGUI by adding a quit button into it.

You can download it from here for test.

GUI for NCBI Blast Parser

2008-09-12T03:29:00.000-07:00

You can see the screenshot of the GUI for NCBI Blast Parser here.

It's difficult to design such a GUI module for NCBI Blast Parser and the module is not finished. It's just a GUI and can not work right now. I will finish it later.

What I worried about is whether the GUI is reasonable. I would appreciate if you can give me some advices.

Amazing things happened!

2008-09-08T02:57:00.000-07:00

To my surprise, there is biopythongui project exists already. The address is http://code.google.com/p/biopythongui/, maintained by "power.jg". And it has been started before August, 2007. However, after checking its code, I found that the project is not active for a long time. Importantly and actually, we are different. See the home page for details. I do not re-invent wheel (thank God). power.jg, the author, he started the project and emphasized on database manipulation. I think it will be a very good thing if he want to continue the project and cooperate with me. I hope that he will continue the project.

BlastGUI 0.1 and BioPythonGUI 0.11 Released

2008-09-07T23:38:00.000-07:00

The BlastGUI 0.1 is released and tested on Fedora 8. I will test it on Windows XP later. BioPythonGUI 0.11 is also released at the same time. In BioPythonGUI, every single module such as, SeqGUI, BlastGUI, can also work as a stand-alone program. The BioPythonGUI main window act as an aggregator for aggregate GUI BioPython modules. In this aggregator, users can view and use all the modules conveniently.
You can download it from https://sites.google.com/site/biopythongui/download.
From here you can view the screenshots of BlastGUI and BioPythonGUI.
I would greatly appreciate if you use BioPythonGUI and send me the feedback.

BlastGUI: the next module

2008-09-06T08:28:00.000-07:00

Currently, NCBI BLAST is a command line tool for both Unix/Linux operating system and Windows operating system. Obviously, it is not convenient for use. So, after the platform of BioPythonGUI been designed, I started this module. However, this is not easy as the previous one SeqGUI, it will spend a few of days. Anyway, I will release it as soon as possible.

BioPythonGUI 0.1

2008-09-04T20:12:00.000-07:00

I am very happey to announce that BioPythonGUI 0.1 is available.
You download it from Here.
In verstion 0.1, there is only one module named Seq available for use. From the beginning of project to now, I am working on the BioPythonGUI frame designing and test. This is important for me and for the BioPythonGUI community (I am sure one day there would be a community exists for BioPythonGUI). And the frame is working now, everyone who wish to be a BioPythonGUI developer can use the frame easily to develop their own BioPython GUI module. In addition, there is a BioPythonGUI template for quick programming. Developers can insert/substitute the content in the template quickly without any considersition on the whole structure of the GUI module. I am sure all of this will be very useful for the development of BioPythonGUI.
Let me know if you have any questions or advices.

The structure test succeed

2008-08-31T07:14:00.000-07:00

In last post, I describe the framework of the BioPythohGUI will use the framework of "PyGTK+ Code Demos", and today, I tested it and succeed. However, there is a bug in the framework, I will upload it tomorrow with bug fixed.

The structure of BioPythonGUI

2008-08-29T17:52:00.000-07:00

The BioPython modules are complicated. They are independent and also of intercommunication. As a GUI of BioPython, I want BioPythonGUI powerful, easy maintained and plug-in enabled. After carefully analyzing the structure of "PyGTK+ Code Demos", I believe that the code structure is reasonable and can be used in BioPythonGUI. So the structure of BioPythonGUI is following:

The GUI module which has complete functional unit is developed independently, called "Functional Unit Module (FUM)", just as the code demos in "PyGTK+ Code Demos";
All the GUI modules are registered in a main window which plays an aggregate role in BioPythonGUI, called "Aggregare Main Window (AMW)", just like the main window in "PyGTK+ Code Demos".

The advantages of this structure:

FUM develop and maintain independently. It is convenient and important for developers;
Everyone in the world can develop their own FUM, this is social web approach. FUM as a plug-in which make AMW powerful;
BioPythonGUI is under the BioPython License. Everyone has the rights to modify the FUM modules and make them better;
AMW as a front-end of all FUM modules which gives users a whole view of FUMs.

GUI Seq

2008-08-29T05:31:00.000-07:00

This is the first BioPythonGUI module named GUI Seq. It inspired by SeqGui.py in BioPython.
GUI Seq has following functions for the biological sequence:

Transcribe
Translate
Back transcribe
Complement
Reverse
Reverse complement

The screenshots is here.
Download here.

What is BioPythonGUI?

2008-08-29T05:04:00.000-07:00

BioPythonGUI is a Graphical User Interface of BioPython.

BioPython is a widely used python module set in bioinformatics. It help researchers:

Parsing files in different database formats
Interfaces into programs like Blast, Entrez and PubMed
A sequence class (can transcribe, translate, invert, etc)
Code for handling alignments of sequences
Clustering algorithms
etc.

However, it's not everyone can use the BioPython, especially ones who do not know much about the programming. How can you expect a professor who never known about any programming to use BioPython to parse the BLAST report file? This is the problem which the BioPythonGUI would solve. I started the project with the goal "Everyone can use BioPython with BioPythonGUI".