Software can make a significant contribution to research, by automating tasks the efficiency of daily work can be improved whilst reducing the rate of error at the same time. SIS develops and maintains a number of software for research data management and data analysis.
openBIS is a FAIR open platform for managing scientific information. Its purpose is to support research data workflows from bench to publication. As a combined data management platform, electronic laboratory notebook (ELN) and laboratory information management system (LIMS), openBIS facilitates reproducibility of scientific results by keeping track of all relevant information on procedures, original and derived research data, analysis methods and knowledge resources. openBIS is a complete data management solution for quantitative research labs.
Software for scientific community
Existing computational software can present a number of issues. Software might be slow, have high memory consumption, be difficult to maintain, or lack usability and visibility due to improper packaging and deployment. SIS provides software solutions to address these, previous examples include:
- HVL CCB (Prof. Franck, D-ITET): Python common code base (CCB) used to control devices used in a High Voltage Lab (HVL) research.
- libsigpatsearch / CAsMap (Prof. Borgwardt, D-BSSE): R and Python packages and an underlying shared C++ implementation of algorithms searching for significant subsets of binary sequences.
- SymPy to C (Prof. Refregier, D-PHYS):
sympy_to_cpackage supports cosmological simulations by translating symbolic equations to a fast C code.
- TopoFilter and HYPERSPACE (Prof. Stelling, D-BSSE): MATLAB packages with an top-down search method over an space of ODE models, based on an ellipsoid-based parameter space sampling method.
UI for existing data or software
SIS can make existing software more accessible by either creating a user interface (UI) or modifying an existing UI. Previous examples include:
- BASEMENT (Dr. Vetsch, VAW, D-BAUG): Desktop application for configuring and running BASEMENTv3 simulations (hydro- and morphodynamic modelling).
- EcoVal (Prof. Reichert, SIAM, Eawag): R Shiny graphical user interface for R package performing ecomorphological assessments intended for use by cantonal administration.
- Entomology (Dr. Eastwood, D-USYS): Web application for digitalization of the photographs and specimen information of several hundred thousand insects.
- MathWiki (Prof. Wagner, D-GESS): Custom Wiki solution for hierarchical annotation of old Hebrew math text.
Ground-up solutions (DB, logic, UI)
Depending on starting resources and requirements, SIS can also provide software solutions built from scratch. Previous examples include:
- datapool (Prof. Maurer, SWW, Eawag) and whdp (Prof. Morgenroth, ENG, Eawag):
A data warehouse for sensor data from field measurements and its Water Hub Data Pool (
whdp) extension adapted for the Eawag's Water Hub.
- emzed (Prof. Vorholt, D-BIOL): LC-MS analysis toolbox (API) focused on ease-of-use for non-programmers.
Big workflow and data management
If data management or processing is presenting issues, SIS can provide custom workflow solutions built on top of the openBIS data management platform. This ensures the reproducibility of results, and that data provenance is recorded. Previous examples include:
- eulerPortal (Prof. Aebersold, D-BIOL): Custom workflow management system, with jobs monitoring and rescuing features, running computations on the Euler computational cluster, connected to openBIS for fetching inputs and storing results.
- Schröder bee (Prof. Schröder, D-BSSE): Background correction pipeline that allows to trigger workflows on the D-BSSE cluster, connected to openBIS for fetching inputs and storing results.