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Quick links

 BeeSpace Navigator version 4 (Software)

 BeeSpace Software Training Workshop (April 2010)

 Arthropod Genomics Symposium (June 2009)

 Final BeeSpace Project Workshop (May 2009)

 Electronic BeeSpace (Education)

BeeSpace Group

The BeeSpace Group consists of core members of the project research team and staff, together with other interested individuals. The group maintains a mailing list and holds laboratory meetings on Wednesdays from 10 am to noon pm in the second floor north conference room of the Institute for Genomic Biology on the UIUC Campus.

BeeSpace email list

The main BeeSpace email list can keep you up to date about project-related events and announcements. List archives and signup are available here.

Fall 2007 lab meetings

The BeeSpace programmers' group meets Wednesday mornings from 10 am to noon in the IGB second-floor north conference room (lunch afterward). An evolving list of topics and dates is below.

Aug 29 Project Overview and Status Report, Bruce Schatz

Sep 5 No Seminar due to NSF Informatics Meeting

Sep 12 Project Internal Strategy Session

Sep 19 Information Extraction from Sequences, Ruth Kantorovitz

Sep 26 Gene Annotator and Microrarray Experiments, Xin He [Powerpoint] [PDF]

Oct 3 BeeSpace Microrarray Experiments, Moushumi Sarma & Cedric Alaux - rough transcript: PDF | MS Word

Oct 10 Gene Summarizer and InsectBase Experiments, Xu Ling [Powerpoint] [PDF]

Oct 17 Adaptive Extraction of Entity-Relations, Jing Jiang [Powerpoint]

Oct 24 Information Extraction from Literature, Yue Lu [Powerpoint]

Oct 31 No Seminar due to NSF DataNet Planning Meeting

Nov 7 Deeper Functional Meta-Analysis, ChengXiang Zhai [Powerpoint]

Nov 14 Discussion of Meta-Analysis for BeeSpace v4, ChengXiang Zhai [Powerpoint], Moushumi Sen Sarma [Powerpoint]

Nov 21 Thanksgiving Vacation

Nov 28 Data Mining & User Personalization, Peixiang Zhao [PDF] & Yuanhua Lv [Powerpoint]

Dec 5 ArthropodBase Workshop (Dec 5-6) (external biologists)

Dec 7 Christmas Party (Friday before Finals)

Spring 2007 lab meetings

A list of topics for the Wednesday morning lab meetings in Spring 2007 appears below.

Jan. 17 - Space Navigation and Functional Analysis, Bruce Schatz [Powerpoint]

Jan. 24 - Entity Summarization (Gene Categories), Xu Ling [Powerpoint]

Jan. 31 - Entity Annotation (Gene Meta-Analysis), Xin He [Powerpoint]

Feb. 7 - no seminar

Feb. 14 - no seminar (snow day)

Feb. 21 - Intrinsic Categorization (Dynamic Map), Brant Chee [Powerpoint]

Feb. 28 - Ontology Annotation (Manual Classify), Dan Xie (Sheng Zhong) [link]

Mar. 7 - no seminar

Mar. 14 - Extrinsic Categorization (Static Map), Qiaozhu Mei [Powerpoint]

Mar. 21 - no seminar (spring break)

Mar. 28 - Concept Switching (towards Regions), Cheng Zhai [Powerpoint]

Apr. 4 - Expression Experiment Pipeline, Amro Zayed

Apr. 11 - no seminar

Apr. 18 - BeeSpace System Software v3, Todd Littell [Powerpoint]

Apr. 25 - no seminar; programmers' collaboration day

May 2 - Molecular dissection using microarrays, Moushumi Sen Sarma

May 9 - Relation Extraction (Fact Extraction from Biological Literature), Jing Jiang

May 21-22 BeeSpace Workshop!!!

Fall 2006 lab meetings

A list of topics for the Wednesday midday meetings that occurred in Fall 2006 is below.

Aug. 30 - Organizational Meeting

Sept. 6 - Entity Summaries, Xu Ling and Jing Jiang [Powerpoint] [PDF]

Sept. 13 - Concept (Word) Summary, Azadeh Shakery [Powerpoint] [PDF]

Sept. 20 - Category (Document) Summary, Brant Chee [Powerpoint] [PDF]

Sept. 27 - Semantic Implementations, Todd Littell [Powerpoint] [Excel spreadsheet]

Oct. 4 - Semantic Algorithms, Qiaozhu Mei [Powerpoint] [PDF]

Oct. 11 - Expression Pipelines, Xin He [Powerpoint] [PDF]

Oct. 18 - No meeting

Oct. 25 - Journal Club (Competitors), read [Text Mining]

Nov. 1 - Journal Club (Annotation), read [Expression Analysis]

Nov. 8 - User Needs, Moushumi Sen Sarma [Powerpoint]

Nov. 15 and 22 - TRAVELS/HOLIDAYS

Nov. 29 - Journal Club (Pathway Extraction), read [Pathway Analysis]

Dec. 6 - Holiday Party

Spring 2006 lab meetings

May, 2006 End-of-Semester Wrap-Up Meetings

Todd Littell, Introducing the next-generation Concept Navigator interface -

Qiaozhu Mei, "Concept Clustering, Summarization and Annotation" - [PPT]

Jing Jiang, "Entity Recognition: Current Status and Summer Plan" - [PPT]

Xin He, "Annotating Gene List from Literature" - [PPT]

Azadeh Shakery, "Multi-Resolution Topic Maps for Information Navigation" - [PDF]

Fall 2005 lab meetings

Sept. 14, 2005 - Todd Littell, "Programming Notes & Advice" - [PPT]

Sept. 28, 2005 - Jing Jiang, "Entity Recognition" - [PPT]

Oct. 12, 2005 - Qiaozhu Mei, "Concept and Theme Discovery Through Probability Models and Clustering" - [PPT]

Oct. 26, 2005 - Azadeh Shakery, "Concept Switching" - [PPT]

Nov. 8, 2005 - Brant Chee, "Partitioning Literature Collections" - [PPT]

Nov. 30, 2005 -
1) Xu Ling, "Automatically Generating Gene Summaries from Biomedical Literature" - [PPT]
2) Xin He, "Information System for Bee Gene Annotation" - [PPT]
3) Moushumi Sen Sarma, "An Interspecific Comparison of Honeybee Brain Gene Expression Using Microarrays"

Spring 2005 lab meetings

Jan 26 Organizational Meeting
Feb 2 Candidate Genes -- Moushumi Sen-Sarma
Feb 9 Regulatory Genes -- Pouya Kheradpour (PDF) / Xu Ling (PPT)
Feb 16 BeeSpace Functionality -- Bruce Schatz
Feb 23 Relationship Matching -- Azadeh Shakery [PDF]
Mar 2 Brainstorm: Navigating Gene Concepts
Mar 9 Entity Recognition -- Jing Jiang [PPT]
Mar 16 Filtering Normalization -- Qiaozhu Mei [PPT]
Mar 30 Genes and Sequences -- Amanda Hummon
Apr 6 BeeBase functionality (outside speaker) -- Christine Elsik [PPT]
Apr 13 BeeSpace Architecture -- Todd Littell [PPT]
Apr 20 Expression Statistics -- Feng Hong [PPT]
Apr 27 Brainstorm: Semantic Text Analysis
May 4 Semester Party
June 6-7 Project Workshop

Archived talks from 2004-2005 meetings

Hong, F. (2005). Introduction to statistical analysis of bee expression data. Presented to weekly BeeSpace Group meeting (April 20). [Powerpoint]

Jiang, J. (2005). Customizing Gene Taggers for BeeSpace. Presented to weekly BeeSpace Group meeting (March 9). [Powerpoint]

Kheradpour, P. (2005). Regulatory Genes: Research Summary. Presented to weekly BeeSpace Group meeting (Feb. 9). [PDF]

Ling, X. (2005). Identify Regulatory Modules from Gene Expression Data. Presented to weekly BeeSpace Group meeting (Feb. 9). [Powerpoint]

Littell, T. (2005). BeeSpace Software: Plans, Design, and Development. Presented to weekly BeeSpace Group meeting (Apr. 13). [Powerpoint]

Mei, Q. (2005). BeeSpace Component: Filtering and Normalization for Biology Literature. Presented to the weekly BeeSpace Group meeting (March 16). [Powerpoint]

Mei, Q., & Jiang, J. (2004). NLP Tools for Biology Literature Mining. Presented to biweekly Bioinformatics group meeting (Nov. 3). [Powerpoint]

Shakery, A. (2005). A Programming Language for Mining Fuzzy Entity-Relation Graphs. Presented to BeeSpace Group weekly meeting (Feb. 23). [PDF]

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