eyegene.ophthy.med.umich.edu

This is the web server of Dr. Julia Richard's glaucoma research lab at the Kellogg Eye Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA.

Latest News

2006.10.31 Publications updated with recent papers.

2006.05.18 The Sequence Chromatogram Assistant is now available to streamline the creation of publication-ready chromatogram graphics of relevant regions of sequence.

2006.02.03 Ed's Unicode Font Guide has now moved to a dedicated website, www.unifont.org, in order to provide better accessibility to the community at large.

2005.12.19 The Eyegene web server finally has a new home on new hardware. Cicada is once again available to authorized users on the new richlab host.

2005.09.25 Ed has written a new Proposal for a Better Font Selection Widget for the Open Source community to review.

2005.08.19 The Font Installation, Fonts, and Utilities sections of the Quick Primer on Unicode and Software Internationalization Under Linux and UNIX have been updated.

2005.07.29 Madeline 2.0 is in the works! Madeline 2.0 is planned as a complete rewrite of Madeline from the ground up with expanded functionality. Click here for more information.

Older News

2005.07.08 A Latest News column has been added to the Unicode Font Guide and several new fonts have been added.

2005.07.05 This News and Events column has been added to the web site.

Research Publications and Presentations

Select List of Publications

Below you will find links to a selection of the most recent publications and presentations produced by the researchers and staff in Dr. Julia Richards lab here at the Kellogg Eye Center:

Software Publications and Presentations

Tools

Web Tools

This section provides links to web-based tools developed in-house.

Cicada Cicada

Cicada is a data entry and retrieval system for marker data used in genetic linkage analyses written by Ed Trager. You can find out more about Cicada here .

Access to Cicada is restricted to authorized researchers at the Kellogg Eye Center. Unauthorized access attempts are logged. Contact Ed Trager if you need access.

Enter Cicada System

Sequence Chromatogram Assistant

The Sequence Chromatogram Assistant is a web-based tool designed to streamline the creation of publication-ready sequence chromatogram graphics. The tool basically runs EMBOSS's ABIView tool for you after you have specified starting and ending bases for the region of interest. The tool modifies the Postscript created by ABIView so that you have less manual work to do to produce publication-ready graphics.

Sequence Chromatogram Assistant

Tiana Mantophasmatodean Gladiator

Tiana is a web-based tool by Ed Trager for rapidly importing tabular data (from spreadsheets, for example) into a database where the data can be examined using the full power of SQL. The tool currently consists of two parts: an importer, and an inspector. For each column in a table, the inspector displays distinct values, counts, and percentages. This allows one to rapidly discern extreme values, non-standardized abbreviations or codes, and other subtle problems that often plague data sets.

Access to Tiana is restricted to authorized researchers at the Kellogg Eye Center. Unauthorized access attempts are logged. Contact Ed Trager if you need access.

Use Tiana

Online Chinese-English Dictionary 网上简繁体汉英词典

A number of online Chinese and Chinese-English dictionaries exist on the web. This one, developed by Ed Trager based on the publically-available CEDICT data, presents results in both simplified (简体字) and traditional characters (繁體字), provides pronounciation in both pinyin (拼音) and zhuyin fuhao (注音符號), and uses carefully constructed search algorithms. These features should make the dictionary useful to mainland, Taiwan, and overseas Chinese, as well as to all students of Chinese.

網上簡繁體漢英詞典

Software

Madeline Madeline

Madeline is a program written by Ed Trager for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. Madeline converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. We are pleased to release Madeline under the GNU General Public License (GPL).

Madeline 2.0 Pedigree Drawing Engine

Older Versions of Madeline Madeline

The stable version (v. 0.935) now detects simple Mendelian inheritance inconsistencies, provides publication-quality multipoint LOD score plotting based on the output from programs like Simwalk2, and features many other improvements.

Madeline v. 0.936 BETA VERSION FOR TESTING DATED 2004.11.04

This new version of Madeline is a bug fix release with some significant improvements as well. Requires a modern, standards-compliant C++ compiler with a good STL implementation such as GNU GCC version 3.3 or better. New features include:

Despite these improvements, please note that this version is still considered a beta version for testing until we have been able to test it more extensively. For documentation, please refer to version 0.935 below.

Download Madeline 0.936 Beta

Madeline v. 0.935

This is the stable version. It features numerous improvements over v. 0.933.

Download Madeline 0.935 Stable Version

Old Version: Madeline v. 0.933

This is the old version which is still available for download by the internet public at large.

Download Madeline 0.933 Old Version

Shuffle

Shuffle is a utility written by Ed Trager in optimized C++ to randomly shuffle a DNA sequence any number of times. The program uses a high-quality portable random number generator presented in Press et al.'s Numerical Recipes in C with a period greater than 2 x 1018. In addition, the program obtains seeds for the random number generator from an entropy pool present on the compute server.

Gt Escherian Quartic Cube

Gt is an X11 text file and non-blocking process output viewer written by Ed Trager. It can be used with Madeline for viewing log files and process output. Gt may be included as part of the Madeline v. 0.935 distribution. Requires GTK+ 1.2 libraries.

Edith Edith Logo

Edith is a professional X11 editor for UNIX and Linux platforms written by Annius V. Groenink that has some particularly nice features for manipulating columns, highlighting multiple items of data, searching using regular expressions, and other features that are extremely useful for editing data files. Compared to an editor like vi, Edith has a much easier learning curve, but still has a fairly extensive set of powerful features useful for advanced data manipulation.

This editor does not originate from our lab here, but we like it a lot and highly recommend that you use this program as the editor to use with Madeline.

The Gladiator Project

Gladiator Gladiator

Gladiator is a new web-based clinical and genetics data entry system being developed by Ed Trager and Ritu Khanna for joint use in the research labs of Dr. Anand Swaroop and Dr. Julia Richards here at the Kellogg Eye Center. Although initially designed for use in these two labs, our long-term goal is to make Gladiator useful for managing the clinical and genetics data for eye disease studies in general.

Unicode

Unicode Primer

Unicode solves the problem of multiple computer encodings for all of the world's scripts, scientific, and mathematical symbols by assigning unique code points in a code space that is much larger than what extended ASCII could accomodate. If your work requires that you reach a global audience in one capacity or another, then you'll want to know about Unicode!

A Quick Primer On Unicode and Software Internationalization Under Linux and UNIX

Unicode Font Guide for Free/Libre Open Source Operating Systems

As Linux and the Open Source philosophy and technologies upon which Linux is based have begun to penetrate new markets world wide, numerous governmental, non-governmental, commercial, and private organizations have been collaborating to provide high-quality Unicode-based fonts to support native language computing. The following is a selective guide to Unicode-based fonts arranged geographically and by script. While ideal for use on free/libre Open Source operating systems, these fonts can also be used on Windows and Mac OSX platforms.

Unicode Font Guide for Free/Libre Open Source Operating Systems

LASi Postscript Printing Engine Project

LASi is a library written by Larry Siden that provides a C++ stream output interface ( with operator << ) for creating Postscript documents that can contain characters from any of the scripts and symbol blocks supported in Unicode and by Owen Taylor's Pango layout engine. The library accomodates right-to-left scripts such as Arabic and Hebrew as easily as left-to-right scripts. Indic and Indic-derived Complex Text Layout (CTL) scripts, such as Devanagari, Thai, Lao, and Tibetan are supported to the extent provided by Pango and by the OpenType fonts installed on your system. All of this is provided without need for any special configuration or layout calculation on the programmer's part. LASi is now being maintained by Ed Trager and Ritu Khanna here at the Kellogg Eye Center.

LASi Documentation Download LASi 1.0.4

Uv Editor

Uv (Uniview) is a lightweight text editor that supports UTF-8 unicode, and provides a small set of advanced text and file manipulation abilities. We decided to start writing Uv after realizing that we were using multiple different text editors, each for different purposes, because no one text editor provided all the features we required.

Uv Documentation uv-1.0.tar.gz

Documentation and Links

Quality Control in the Linkage Analysis Data Pipeline

In February of 2003, Ed Trager gave a talk to a group of graduate training grant recipients from the Department of Biostatistics on quality control issues and solutions for preparing linkage data for statistical analysis. This link will take you to the slides used in that presentation.

Quality Control in the Linkage Analysis Data Pipeline

Richards Lab Bioinformatics Software Documentation

These are links to the documentation distributed with various packages that are available on our servers:

Unix Tutorials

Sooner or later, researchers in the life sciences often need to move beyond the limited world of computing on a standard Windows PC and tackle the initially daunting, but in the long run rewarding, world of Unix-based computing.

The following link from the Electronic Engineering Department at the University of Surrey, Guildford, UK, is a highly recommended "how to" resource that will help you come up to speed on UNIX quickly:

UNIX Tutorial for Beginners

Our link below will provide you with a conceptual overview, as well as in-depth coverage of some of the more important tools that you will need to know to work in a modern, secure UNIX-based computing environment:

Richlab UNIX-based Computing Resources Tutorial

The above tutorial includes, but is not limited to, the following topics:

The following link provides baseline instructions for using Phred, Phrap, and Polyphred in the Richlab Unix computing environment:

Phred/Phrap/Polyphred Instructions (PDF)

People

Principle Investigator

Dr. Julia Richards

Dr. Julia Richards

The research program of Dr. Julia Richards focuses on the underlying causes of hereditary eye disease. Her research has a long-term emphasis on the group of diseases classified as glaucoma, one of the leading causes of irreversible blindness in the United States. Several recent breakthroughs in gene mapping and cloning have resulted from her collaborations with glaucoma specialist Paul R. Lichter, MD, biostatistician Michael Boehnke, PhD, and researchers at other institutions including Stanford, University of Oklahoma, and UCSF.

Her work on characterizing specific glaucoma genes and their role in glaucoma and related phenomena is paralleled by efforts to better understand the clinical characteristics associated with particular genes and mutations. Studies at the level of genes, cells, animals and people all assist in our efforts to sort through the underlying causes of the hereditary glaucomas and evaluate the relationships between the glaucomas and a variety of abnormal developmental processes, both ocular and non-ocular. Genome scanning, positional candidate cloning, gene mapping, mutation screening, expression studies including promoter analysis and studies of protein products, cell culture and transgenic animal models of human disease, computer informatics, clinical characterization, genetic counseling and patient education all contribute to advances in understanding the underlying causes of glaucoma and relating those findings to clinical practice.

Select Publications

Staff

Ed Trager Hemant Pawar David Reed Frank Rozsa Kathy Scott

Lab Alumni

Rosa Ayala Kanjana Soongswang