Thuwal, Makkah, Saudi Arabia
Interested in connecting research results with reference bioinformatics datasets, such as UniProt, HMDB, and ModelSEED
I had to leave KAUST after 10 years of service, since my heart is with KAUST I will not mark an end date here in LinkedIn. I was accepted to KAUST by Professor Vladimir Bajic in 2016. Early years I helped Vlad’s students with building indicies and writing query interfaces for their research findings. Before leaving us Vlad asked me to support CBRC efforts for clustering and annotating genes found in public metagenome sequencing data. Initially I worked for a study we named Earth Microbiome Gene Catalogue, later we concentrated on Ocean samples of this study and published our findings, naming KMAP Global Ocean Gene Catalogue. Recent years we worked for a study with a larger set of samples that we named KMAP Biosphere Gene Catalogue. We have indexed the clusters with their annotations and included in the query interface we have been developing for the last six years; habitats.kaust.edu.sa. In addition to many summaries, we worked on summarizing pathway completions of all samples for all KEGG modules, based on EBI MGnify team’s pathway graphs [1, 2]. From my new location in Turkey with my limited computing environment, I have been striving to help maintain the habitats web interface. Earlier we developed few webservices for the ChatGPT based chatKMAP project, we would like to maintain them as well. Most recently we have worked on query interfaces for Biosphere Gene Catalogue MAGs, their annotations and clusters, we would like to complete this work as well. During the pandemic time, I also contributed to CBRC CovMT project; with solving scalability issues project’s team met, with reimplementing its indices and query interface with better software stack; covmtdev.kaust.edu.sa. I kept updating the sequencing metadata indices and recalculated the mutation summaries with regular intervals until April 2026. [1] https://github.com/EBI-Metagenomics/kegg-pathways-completeness-tool [2] https://habitats.kaust.edu.sa/summary?table=kegg-module-completion-brite-groups-hqmags
Web Production Team Maintenance of high volume Java web services server, Jdispatcher, and its web interface: During my first year I worked more on stability issues such as concurrency problems, resource leaks, and safe efficient use of memory. I also located and fixed performance problems such as simultaneous parser jobs for the same result and duplicate/unnecessary calls to external programs. In my second year I spent considerable energy for smooth transition of the web interface when Institute web sites went through a major redesign. I implemented basic web-theme support, and used Ajax calls to improve selection of the result views. Listed below are some of the tasks I worked later in my second year and in year 2014. - Prepared WADL description for the REST-based web services interface - JAXB implementation of Data Access Objects for xml configuration files, in order to support Xinclude - Implemented thread pools support for the executor service, for more controlled execution of tasks - Located and fixed a failover/connection strategy problem for a JMS queue that was preventing servers recovery, for example after a file system problem - Updated the execution workflow of the ncbiblast tool to support all available output formats
EMBOSS Team: Soaplab bioinformatics web services server: - Maintained the legacy version of the server while its reincarnation was under development, located and fixed an important memory leak that was preventing stability of the server - Contributed to the development of the new version of the Soaplab software; in using the Java API for XML Web Services(JAX-WS), updated initial implementation of the service classes for thread safety, implemented support for the EMBOSS programs and for the LSF load sharing system - Developed a new Web Services interface that different from the Soaplab classic interface the input and output types of the supported tools were defined at WSDL level - Migration of the servers to better platforms as they became available - Implemented tests for better coverage of all services - Helped users with their queries EMBOSS bioinformatics software project: - Updated the algorithm of 'needle' sequence alignment program to support end-gap penalties - Implemented efficient multi-pattern search algorithm Rabin-Karp, for seed-finding in 2 search programs; the longest exact matches search program 'wordmatch' and the banded Smith-Waterman search program 'supermatcher' - Implemented data access methods for few bionformatics web services servers - Contributed to the implementations of support for NGS data formats - Bug fixes and improvements to the Jemboss module, a Java/Swing based GUI and Java Web Services server for EMBOSS programs
Main product of Lion Bioscience Ltd, SRS, was a scalable data integration platform for bioinformatics data. My tasks were more focused on the component for integration of third party analysis tools, which were used to further analyse results of user queries. - Worked on improving the performance of SRS and had successful results for its indexing, query and sort performance - Located and fixed concurrency problems, and memory leaks in SRS servers (initially CORBA server, later SOAP Web Services server) - Worked on CGI based and JSP based web interfaces - Developed workflow support and collaborated with colleagues in a sister company in Heidelberg to implement features required for the workflows they were developing - Implemented load-sharing systems support for the tools module
System administration responsibility of a mainframe computer. Helped my colleagues in reducing the processing time of a time critical algorithm using dynamic programming.
Worked in a multi-national research project; writing C programs for guiding simulated entities in distributed simulation environments.
IT support role, initially in the Graduate School, later in a CAD/CAM laboratory