Featured Publications

• Van-Giang Trinh, Belaid Benhamou, Sylvain Soliman (2023). Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding. Theoretical Computer Science, 971:114073.
• Marek Ostaszewski et al (2021). COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology, 17 (10):e10387.
• Elisabeth Degrand, François Fages, Sylvain Soliman (2020). Graphical Conditions for Rate Independence in Chemical Reaction Networks. In CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology.
• Sara Sadat Aghamiri et al (2020). Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics, 36 (16):4473-4482.
• Sylvain Soliman (2016). A structural perspective on the dynamics of biochemical systems. Accreditation to supervise research, Université Paris Sud - Orsay.
• Sylvain Soliman (2013). A stronger necessary condition for the multistationarity of chemical reaction networks. Bulletin of Mathematical Biology, 75 (11):2289-2303.
• Sylvain Soliman (2012). Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem. Algorithms for Molecular Biology, 7 (1):15.
• François Fages, Sylvain Soliman (2008). Abstract interpretation and types for systems biology. Theoretical Computer Science, 403 (1):52–70.

Recent Publications

• Van-Giang Trinh, Sylvain Soliman, François Fages, Belaid Benhamou (2025). On the Trap Space Semantics of Normal Logic Programs. In Daniela Inclezan Martin Gebser, Francesco Ricca, editor, ICLP 2025 - 41st International Conference on Logic Programming, pages 294–319.
• Ouissem Saidi, Nicolas Gaudenzio, Sylvain Soliman, Fabien Crauste, Anna Niarakis (2025). DigiDermA: Modeling Cellular and Molecular Interactions in Atopic Dermatitis. In JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques.
• François Fages, Mathieu Hemery, Sylvain Soliman (2025). On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry. ACM Communications in Computer Algebra, 58 (2):15-22.
• Van-Giang Trinh, Belaid Benhamou, Sylvain Soliman, François Fages (2024). Graphical conditions for the existence, unicity and number of regular models. In Pedro Cabalar, Francesco Fabiano, Martin Gebser, Gopal Gupta, Theresa Swift, editor, ICLP 2024 - 40th International Conference on Logic Programming, pages 175-187.
• Anna Niarakis et al (2024). Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology, 14.

Teaching

I taught in the following frameworks:

• in the Paris Computer Science Masters (M2 Research), I was in charge of the Constraint Programming course;
  • class 1 - Introduction to CLP, operational semantics, examples
  • class 2 - CLP: fixpoint semantics
  • class 3 - CLP: logical semantics, CSP: solving by simplification and domain reduction
  • class 4 - CLP: the Warren Abstract Machine, CSP: Symmetries
  • class 5 - CLP: typing; CHR; Programming project discussion; MiniZinc and CLPZinc
  • class 6 - CC: examples, operational and denotational semantics
  • class 7 - CC: linear logic semantics; LCC
  • class 8 - LCC: logical semantics, links with CHR; EMoP: modules for LCC/CC/CLP

• I used to be for several years teaching assistant for Java classes corresponding to the Informatique Fondamentale lessons of Jean-Jacques Levy at École Polytechnique. Then I taught in the third year course about “Constraint-based Modeling & Algorithms for Decision Making”, the 2nd year MODAL “Programming in the Language of Life” and the Bachelor course on “Constraint Logic Programming” (plus some other TA things here and there)

I also supervise some internships on the dedicated page of the Lifeware team.

Links

Mac and Mac OS X

• Though I am mostly using Macs, I don’t use much Apple applications. Therefore, besides the software listed in next section and mostly obtained through Nix-darwin and Homebrew, I use:
  • Firefox,
  • Hammerspoon,
  • VLC,
  • LibreOffice,
  • Gimp.app and Inkscape,
  • iTerm2 or kitty (when I was still using vim)…

Other software

• Debian remains my preferred Linux distribution, for philosophical as well as practical reasons (package management, administration scripts, security updates, etc…);

• I used to be from times to times under OpenBSD, the best platform for security;

• I used Vim for more than twenty years as text editor, for almost everything (mail, web pages writing, programming, etc…), and most of the time its newest incarnation NeoVim. I still love its modal design and fast response. The best book I’ve found on the topic is by far Practical Vim by Drew Neil;

  I developed a prolog mode (syntax highlighting, and more…) that extends the standard prolog mode. It also provides a few useful key bindings and a better detection of prolog files (.pl not defaulting to Perl mode anymore);

• I use Exuberant Ctags to move around the many heterogeneous (typically C and prolog) source files of my applications when I don’t have a good enough Language Server Protocol implementation available. I thus needed to add a few lines to my .ctags config file to get the behavior that I wanted;

• mutt was my mail-client (MUA) and slrn my news-reader. They have a quite close, and very customizable, interface;

• These days I’m mostly living in Emacs (Doom Emacs) using mu4e for mail, elfeed for rss, magit/vc-mode and AucTeX for their respective features, and of course org-mode…

Languages

• I mostly use LaTeX when it comes to producing documents, and for some time I’ve been very happy with the beamer class for slides, that I did customize for our internal needs. I do generate some of these LaTeX slides from org-mode source;

• Besides SWI Prolog and C, the language I mostly use, especially for scripts, is Python, which replaced Perl and its wonderful CPAN archive with its package index. I must admit to also write some shell-scripts, which is made quite easy thanks to ZSH resources like zsh lovers or zsh tips;

• concerning HTML, there are many good resources like the W3C web site, but I have to link A list apart a wonderful design blog, especially all the content by Ethan Marcotte, and HTML5 Rocks a Google project with everything you need to know about HTML5.

The game of Go

See my dedicated post

Blackjack

Everybody now wants to play Hold’em, but…

• Gambling Book Reviews: very good book reviews, with among others BJ books;

• The Gamemaster Blackjack School: a free 24-lesson class on card counting;

• Knock-out Blackjack is the book that taught me card counting.

• Blackjack Review Network: an excellent page with very good thematic forums;

Dance

• I enjoy a lot dancing (and listening to) Cuban Salsa

  • Fiesta Cubana.net is the (French) reference forum;

• Argentine Tango is now rather a nice souvenir…

  • Mephisto Tango: an association providing high quality classes;

  • Tango-L: the authoritative mailing-list about Argentine Tango;

Useful web pages

• To make reservations or just check schedules/rates, I used to use Trainline instead of the official SNCF-Connect site from the French railways company, but since they were bought out their customer support has gone ugly and they leak private data to FB and such, so… use 12train instead, it’s nice and clean!;

• Webster’s online dictionary, a reference, as well as dictionary.com and JDIC (English-Japanese, Japanese-English, and more…);

Contact