I can speak, read, and write in English
, C++ and some machine codes.
allow one to perform tasks in a research setting.
- Offer comprehensive bioinformatics services to researchers,
- Perform autonomous project management -- including milestones, tickets, & roadmaps,
- Establish intelligence investigation for rational decisions,
- Edit a manuscript,
- Review a manuscript,
- Write & author a manuscript,
- Write scholarship applications, and
- Read content.
Write intention letters before submitting papers,
- Read and grasp everything in The Elements of Style (life-time achievement),
- Actually be a peer for a peer-reviewed journal, and
- Rule the world.
Biology plus informatics
harnesses available computer software and hardware to perform data analysis in biomedical sciences. My specialities are
- bioinformatics toolboxes (emboss, biopython, bioperl, AMOS),
- molecular displays (pymol),
- databases (geneontology, EBI, NCBI, KEGG, short read archive),
- machine learning (string kernels, support vector machines, adaboost),
- sequence alignments (MUMmerblast, blat, dottup),
- high-throughput (Illumina, Roche 454, SOLiD, Helicos) sequencing data analysis with reference sequences (bowtie, bwa, maq, samtools), and
- high-throughput sequencing data analysis without reference sequences (Velvet, ABySS, Newbler, EULER-SR, Ray).
Free/Libre Open Source Software
changes the landscape of available software and toolchains. My proficiencies are
- software craftsmanship (vim, git, ssh, gcc)
- command-line tools (mutt, links2)
- collaborative work (git, openldap, apache, webdav, subversion, trac, mediawiki, mailman, sourceforge),
- database software (mysql, postgresql, sqlite),
- operating systems & tools (ubuntu, debian, centOS, fedora, gentoo, lvm, bash, gnu software, linux kernel, gnome),
- data & user security (openssh, rsync, crontab, sshfs),
- compilers & friends (automake, autoconf, gcc, gdb, valgrind, make)
- open statistics (R, cat, uniq, wc, awk),
- text editors (vim, emacs),
- message passing interface (Open-MPI and MPICH2),
- document preparation (latex, xml, xsl, docbook), and
- software design & implementation (python, ruby, bash, C, C++, java, lua, php, perl, doxygen, javadoc).
High Performance Computing
is a cornerstone for the society advancement, enabling discoveries with software simulations. My capabilities include
- compiled programming languages (c, c++),
- compilers (icc, gcc),
- parallel paradigms (MPI, OpenMP),
- low-level stuff (SPARC assembly, x86 assembly, page faults, on-demand paging)
- scheduling with fair-share algorithms (Sun Grid Engine)
- UNIX (sockets, processes, threads, shared memory with mmap),
- MPI implementations (Open-MPI, mpich2, mvapich), and
- MPI standard version 2.2.
Thu May 5 14:40:06 EDT 2011