Updated .NET Bio 1.10 Installers and added 1.10 training materials

7/23/2013
During our training course our instructor discovered some issues in .NET Bio 1.10 that are now addressed and with that we have new 1.10 installers uploaded today.

1) Some Fasta files would not load if they had sequences with only gaps and then sequences with RNA because it would assume DNA for the gaps and then fail to load RNA sequences.

2) The new parsers didn't have DEFAULT public constructors which caused an internal exception during startup (which was handled so it didn't crash). The constructors were added so the parsers show up in the sequence list now.

Training Course Using new .NET Bio 1.10 in Manizales, Colombia.

7/02/2013
The workshop is July 9-11th.
There are details on the BIOS website here.

.NET Bio 1.10 released!

6/27/2013
The development and testing of .NET Bio 1.10 is now complete and we have released this updated version. You can get the installers for .NET Bio, the Biology Extension for Excel, and the Sequence Assembler here. If you do encounter an issue please report this under the issues menu. For comments or questions use the discussions menu. We appreciate all the hard work by this community to get the release completed.

Open Source Lab Launches in Australia - featuring .NET Bio

6/12/2013
Queensland University of Technology (QUT) launched the Open Source Software Group and Virtual Lab at the university’s new Science and Engineering Center. There is a detailed blog on the Microsoft Research site here.

Alpha release of .NET Bio 1.1!

5/7/2013
The installers for .NET Bio, Biology Extension for Excel, and Sequence Assembler are on the downloads tab today. Please give these a test with data you may have. If you discover any issues please create a new issue on the issue tracker tab. The release is dependent on getting good validation at this point. Thanks in advance.
Here is a link to the location Alpha .NET Bio 1.1

Updated BioExcel Installer Released

5/16/2012
A new version of the installer for the .NET Bio Biology Extension for Excel 1.01 has been uploaded today. This version removes the dependency check for NodeXL. While NodeXL is required to draw proportional Venn diagrams indicating the relative proportions of unique and non-unique sequences contained in .BED files (see documentation), it is not required for the other functions of this add-in. The dependency was removed to streamline installation for those that do not use .BED file functionality.

.NET Bio 1.01 released!

4/16/2012
The .NET Bio team is pleased to announce the latest release of the .NET Bio library, Excel add-in and Sequence Assembler demo application. This minor-version release fixes a range of bugs reported in version 1.0 as well as adding new new features such as AB1 and SFF file format parsing, better output and help for command-line tools, and comprehensively revised documentation. Please refer to the release notes for more details.

Cornell training samples

3/26/2012
We had a wonderful 2 day course at Cornell. Thanks to Jarek for hosting us during this training. This is the folder of samples from our trainer Mark from the Ithaca, NY training course.

.NET Bio training at Cornell University in Ithaca, N.Y.

2/28/2012
We will be having a .NET Bio training course March 22nd and 23rd at Cornell University in Ithaca, NY. You can register for the course at this site.

NuGet package available for .NET Bio

2/24/2012
We now have a NuGet package available for .NET Bio here. NuGet allows you to add dependencies to a Visual Studio project directly from an online source - such as bio.dll for instance :) For more information, see this blog post which shows you step-by-step how to use this new distribution mechanism.

Using a dot plot to view consensus between sequences

2/1/2012
A visual method to view consensus between sequences is to use a dot plot. See thisblog about dot plotting genetic sequences with .NET Bio. This is a series of blogs with code samples to help you see the potential in utilizing .NET Bio. Enjoy!

Demo files from Redmond .NET Bio workshop

12/7/2011
Here is the zipped folder of the demo files from our December 2011 workshop in Redmond. If you have any questions or issues with the files please post in the discussion forum and we can address for everyone. Thanks to all of you who attended the course. Mark and I are anxious to see your new contributions to the project.

WPF+PRISM+.NET Bio

11/28/2011
Check out this blog post by our .NET Bio trainer, Mark Smith. It utilizes prism coupled with Windows Presentation Foundation and incorporates .NET Bio. As Mark notes - this post is the start of a series which will combine these efforts and attempt to give others some helpful ideas on doing bioinformatics with .NET – and creating visualizations with WPF!

SeQCOS project announced

11/09/2011
There is a new project (SeQCoS) built using .NET Bio and now shown in our related projects link. An overview is detailed in this blog post Building a .NET Quality Control Tool for Next-Generation Sequencing Technologies. An example usage scenario in which SeQCoS and .NET Bio could be utilized is for de novo assembly of genomes. Past experience has shown that while performing a de novo assembly, a reduced data set of high quality reads will produce better assemblies than a higher volume data set of lower quality. Given a collection of input reads, a user can first run SeQCoS to evaluate the quality of the sequencing reads and make the necessary adjustments to improve data quality (e.g. trim/discard poorly performing sequences). Next, the user can use PadeNA de novo assembler tools, which are packaged with .NET Bio, to perform de novo assembly.

.NET Bio Workshop in Redmond, WA - Dec. 5th and 6th

10/26/2011
We will be holding a 2 day workshop on .NET Bio December 5th and 6th in Redmond, WA, at the Microsoft campus. The course will start at 9:00AM both days and will be located in room 1927 in building 99. The address is 14820 NE 36th Redmond, WA. You can view additional information and register for the course on our events page. The course has no cost and we ask that you register only for logistics planning of the course. As a reminder we do ask that you come prepared for the labs by installing Microsoft Visual Studio 2010 as indicated on the registration and information page. If you have any questions you can contact our community program manager at (425) 538-4921.

Samples available from UCSD workshop

10/21/2011
Here are the samples from our UCSD workshop that our trainer mentioned he would make available.

Samples available from Phoenix workshop

9/12/2011
During our Phoenix workshop Mark, our trainer referenced several samples that he will be making available. You can get these samples here. I hope you all enjoyed the workshop. I did send an attendee survey out via email today in case you didn't get an opportunity to complete one after the course. We would love to hear your thoughts on our course and ideas about what you think we could do to improve it.

Microsoft Biology Foundation Workshop October 20-21 2011, San Diego, California

8/18/2011
We will be holding a 2 day workshop on MBF in October at the University of California, San Diego campus. The course will start at 9:00AM both days and will be located in room 4004 in Atkinson Hall. You can view additional information and register for the course on our events page. The course has no cost and we ask that you register only for logistics planning of the course. As a reminder we do ask that you come prepared for the labs by installing Microsoft Visual Studio 2010 as indicated on the registration and information page. If you have any questions you can contact our community program manager at (425) 538-4921.

Microsoft Biology Foundation Workshop September 8-9 2011, Phoenix, Arizona

8/4/2011
We will be holding another 2 day workshop on MBF in September on the Arizona State University campus. The course will start at 9:00AM and will be located in the auditorium at Biodesign Institute. You can view additional information and register for the course on our events page. I'll post an additional course announcement sometime next week as well. Looking forward to seeing some of you there and hearing what you have to say about MBF V2.

MBF Coding Contest winner!

7/28/2011
We received a terrific entry for our MBF V2 Beta 1 coding contest from Kajal Das. As the winner of the contest he was awarded an Xbox 360 4GB with Kinect for his efforts. His DNA and RNA Sequence Annotation Studio application takes advantage of the GenBank and FASTA parsers, as well as GenBank Formatter and other features of our beta. His application allows one to:
View the complete sequence, including a nice zoom feature
View annotations either in whole or selectively
Create/edit/delete annotations
Save the modified sequence in GenBank format
You can see his project on CodePlex at http://seqannotationstudio.codeplex.com/

When asked about his experience using our beta he had this to say "First of all, I have been waiting for a long time for something like this to come from Microsoft. I had heard about BioPerl, BioJava, etc. Now, MBF opens up the path to new possibilities for the .NET developers." "Overall, I have had a great experience while working with MBF and developing the application using MBF. I enjoyed it thoroughly even being up till 2 o'clock in the morning for almost 10-12 days. "

Our congratulations go out to Kajal and we hope to see more of his work here on our project. Our version 2.0 is nearly ready, although I don't have a final date at this point in time.

Recap Microsoft Biology Foundation Workshop July 7-8 2011, Brisbane, Australia

7/13/2011
We had a small but enthusiastic audience for our 2 day workshop held in Brisbane, Australia last week. Besides the discussions on parsers, formatters and C# .NET our trainer managed to cover a bit of Trident which garnered some interest among the students. We had attendees from CSIRO, Garvan Institute of Medical Research, and of course UQ and QUT. We hope to see some items aired during the course out on the discussion forum shortly as people digest the information provided. Many thanks to several people at QUT and UQ for assisting us in putting on a great workshop. The hospitality was very welcome. For those that registered and were unable to attend we will be having more workshops but perhaps not as convenient for those of you located in Australia. A reminder for those that haven't already submitted their entries for our coding contest, the deadline is this Friday July 15th at 5:00PM PST.

Schedule Update Microsoft Biology Foundation Workshop July 7-8 2011, Brisbane, Australia

6/30/2011
There has been a change to the start times for the MBF workshop held on July 7th and 8th in Brisbane. It will be at 09:00AM not 08:00AM as listed on our site. We will be in the large seminar room 3.142 Queensland Bioscience Precinct. The directions to the venue are here. This change will also adjust our class schedule which we will communicate at the site. Looking forward to seeing many of you there.

Microsoft Biology Foundation Workshop 2011, Brisbane, Australia

6/2/2011

We are holding a two day MBF workshop in Brisbane, Australia on July 7th and 8th in conjunction with the 2011 Winter School in Mathematical and Computational Biology hosted by The University of Queensland. You can find details on the courses and a link to the registration site here. The course will be focused on version 2 of MBF and the changes from version 1.

Post Beta 1 Drop now available under source code tab

5/19/2011

Our development team has been progressing on their push to complete version 2.0 of MBF. To that end, another milestone drop was just published under the source code tab. You should understand this is a milestone drop and as such will have issues and is not to be used for production work. Please do report any issues you encounter on the issue tracker tab. You should base any new contributions on this version of course.

Microsoft Biology Foundation Workshop 2011, Cartagena, Colombia

5/16/2011

Our third installment of the MBF training workshop is taking place in Cartagena, Colombia May 16th and 17th. This course incorporates the new features found in our V2 beta 1 release. Descriptions of the event are located here http://research.microsoft.com/en-us/events/mbf2011-cartagena/default.aspx

MBF Coding Contest using MBF V2 beta 1

5/11/2011

We are holding a contest to find the best bioinformatics and genomics application built on our just released MBF 2.0 beta 1. The contest ends July 15th at 5:00PM with the winner announced on July 27th. You can see the contest details here http://research.microsoft.com/en-us/projects/bio/mbfcontest.aspx. The winner will receive an Xbox 360 4GB console with Kinect.

Announcing the beta 1 release of MBF 2.0 today.

4/22/2011

For those of you who evaluated our developer preview in December of last year enjoy! This is the first significant update since MBF 1.0. We do appreciate the contributions made to date. Here are some highlights included in this beta.
  • Increased capacity for de novo assembly of larger and more complex species than V1
  • Addition of comparative assembly functions for characterizing genetic diversity within or between species
  • Core object model improvements for smaller memory footprint and increased parallel processing
  • Parity with all version 1.0 tools and features
  • New command line tools to help with genome assembly
  • Updated documentation

We will be having updated training based on our beta in the near future. As well as additional training courses. As always we appreciate your participation and feedback

Rick Benge for the MBF team

Thank you for a great MBF workshop, April 2011

Microsoft Biology Initiative and RENCI have hosted a two day workshop at the Renaissance Computing Institute in Chapel Hill, North Carolina.
Mark Smith http://www.julmar.com/blog/mark, our instructor, did a great job of presenting the materials and engaging the audience regardless of the variety in programming backgrounds. Most attendees loved the code along sessions! You can find all the workshop samples in Mark's blog. You can also download all MBF training materials including slides and hands-on labs from http://research.microsoft.com/en-us/projects/bio/training.aspx.

Announcing: MBF two-day workshop, April 19-20, Chapel Hill, NC

3/2011

The Microsoft Biology Initiative and the Renaissance Computing Institute (RENCI) are hosting a two-day workshop on the Microsoft Biology Foundation. The MBF workshop will be held at the Renaissance Computing Institute in Chapel Hill, North Carolina, on April 19 and 20, 2011. This workshop will include a quick introduction to Microsoft Visual Studio 2010, the .NET Framework, C#, and the MBF object model. Attendees will participate in hands-on labs and write a sample application that employs the file parsers, algorithms, and web connectors in MBF. The workshop is open to everyone and registration is free of charge. For complete details and registration please visit: http://research.microsoft.com/en-us/events/mbf2011-chapelhill/.

Thank you for a great MBF workshop March 11

3/2011
We had a great turnout! Read all about it in our Microsoft Biology Initiative Blog: http://blogs.msdn.com/b/mbi/archive/2011/03/16/thank-you-for-a-great-mbf-redmond-workshop-march-11.aspx

Announcing: MBF one-day workshop, March 11, Redmond, WA

2/2011

The Microsoft Biology Initiative is hosting a one-day workshop on the Microsoft Biology Foundation. The MBF workshop will be held at the Microsoft Conference Center in Redmond, Washington, on March 11, 2011. Attendees will participate in hands-on labs and write a sample application that employs the file parsers, algorithms, and web connectors in MBF. The workshop is open to everyone and registration is free of charge. For complete details and registration please visit: http://research.microsoft.com/en-us/events/mbf2011/.

Announcing the release of MBF v2.0 Preview

12/2010

We are excited today to give you a preview of our V2 of the Microsoft Biology Foundation. This release is intended as development evaluation only.

In this release, we have fixed some bugs and have implemented / improved some of the below features (please note this is not a complete list, as some items are still in progress):
  1. BAM extension scenarios and paired end support
  2. MUMmer optimizations to support large genome assembly
  3. Object Model changes to use ISequence : IList<byte>
  4. Optomization work:
    1. Memory profiling and analysis on MBF
    2. PaDeNA memory optimizations
    3. Sequence optimizations (including non-string & non-character)
    4. MUMmer optimization based on sequence
    5. Object Model optimizations
    6. More scenarios for collection of memory & perf profiles

To fully enjoy this release, and to avoid any conflicts, we strongly recommend that you fully uninstall the V1 of Microsoft Biology Foundation before installation of V2.
We also are aware of few issues in this code, the ones that might affect your installation are listed below:
  1. The DLL Version of MBF is incorrectly reported as 1.0.0.0
  2. The installer installs MBF in a directory called 2.1 (and not 2.0).

We hope you enjoy this preview, and we would love to have your feedback via our Community Forum or Discussions in CodePlex.

The MBF Team


Last edited Sep 17, 2013 at 3:51 PM by Rickbe, version 20

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