MOTIVATION: Functional screening of patient-derived T cell receptor (TCR)-neoantigen pairs via co-culture experiments is a way to design personalised immunotherapy or to investigate its mechanism of action. Current computational toolkits can either generate and prioritise candidate epitopes from tumour variants or count barcodes in sequencing data. However, they lack modules to support experimental screening, such as sample demultiplexing, construct quality control, and downstream analysis. To bridge these gaps, we present pepitope, an R package that integrates minigene library generation, sequencing-based quality control (QC), and differential abundance analysis of co-culture screens into a single software package within the accessible R/Bioconductor ecosystem. RESULTS: pepitope workflows include the extraction of mutant and reference peptides with customisable flanking regions from tumour variant calls using Bioconductor annotation resources; demultiplexing and barcode counting for construct QC; and negative-binomial-based differential testing built on DESeq2 to identify immunogenic epitopes in TCR co-culture assays. By remaining within R, pepitope lowers the barrier for lab-based biologists familiar with R and Bioconductor to perform end-to-end co-culture screen analyses without needing dedicated computational support. AVAILABILITY: pepitope (R ≥ 4.5.0) is freely available on GitHub under the GPL-3.0 license, with detailed vignettes hosted at https://mschubert.github.io/pepitope/. Installation is facilitated via the remotes package in R.

Many basic properties in Tutte's flow theory for unsigned graphs do not have their counterparts for signed graphs. However, signed graphs without long barbells in many ways behave like unsigned graphs from the point view of flows. In this paper, we study whether some basic properties in Tutte's flow theory remain valid for this family of signed graphs. Specifically let $(G,\sigma)$ be a flow-admissible signed graph without long barbells. We show that it admits a nowhere-zero 6-flow and that it admits a nowhere-zero modulo $k$-flow if and only if it admits a nowhere-zero integer $k$-flow for each integer $k\geq 3$ and $k \not = 4$. We also show that each nowhere-zero positive integer $k$-flow of $(G,\sigma)$ can be expressed as the sum of some 2-flows. For general graphs, we show that every nowhere-zero $\frac{p}{q}$-flow can be normalized in such a way, that each flow value is a multiple of $\frac{1}{2q}$. As a consequence we prove the equality of the integer flow number and the ceiling of the circular flow number for flow-admissible signed graphs without long barbells.

MOTIVATION: High performance computing (HPC) clusters play a pivotal role in large-scale bioinformatics analysis and modeling. For the statistical computing language R, packages exist to enable a user to submit their analyses as jobs on HPC schedulers. However, these packages do not scale well to high numbers of tasks, and their processing overhead quickly becomes a prohibitive bottleneck. RESULTS: Here we present clustermq, an R package that can process analyses up to three orders of magnitude faster than previously published alternatives. We show this for investigating genomic associations of drug sensitivity in cancer cell lines, but it can be applied to any kind of parallelizable workflow. AVAILABILITY AND IMPLEMENTATION: The package is available on CRAN and https://github.com/mschubert/clustermq. Code for performance testing is available at https://github.com/mschubert/clustermq-performance. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Steinberg's conjecture states that planar graphs without 4- and 5-cycles are 3-colorable. This conjecture, though disproved recently, has motivated a lot of work in the literature. A plane graph is a planar graph $G$ together with an embedding of $G$ into the Euclidean plane. A 7-cycle $C$ of a plane graph is ext-triangular if it is adjacent to a triangle $T$ such that the areas inside $C$ and inside $T$ have no intersection. In this paper, we prove that plane graphs without 4- and 5-cycles are 3-colorable if they contain no ext-triangular 7-cycles, which improves a number of known results. In particular, our result implies that (1) planar graphs without 4-, 5-, and 7-cycles are 3-colorable, and (2) planar graphs without 4-, 5-, and 8-cycles are 3-colorable.

Digital tabletops are gaining increasing relevancy within commercial and educational sectors. These devices, with their multi-touch surfaces, can support collaborative activities while maintaining natural face-to-face communication. However, we still know little about possible learning outcomes and the situations they favor. We have conducted a study to explore how group activities on tabletops could potentially encourage collaboration on tabletops. We have particularly focused on the potential of tabletops to favor knowledge transfer, which can be translated to the question how knowledge might be assimilated, understood and transferred in the best way. This paper presents a comparative study of a learning session using concept-maps on tabletops and a learning session using traditional paper and pencil tools. The comparison revealed a tendency for the tabletop-environment to effectively support knowledge transfer.

International audience

The design and measured performance of an interference suppression device is described. The device is intended for usage in a non-power controlled CDMA system to reduce "near-far" effects. The device demodulates the chips of a strong interfering user and subtracts this locally generated interfering spread spectrum signal from the received signal. For large signal-to-noise ratios (SNR) the device reduces the interference considerably. The reduction is limited by the 20 dB dynamic-range of the passive power-combiner which is used for signal subtraction. The interference suppression capability degrades with decreasing SNR. For very low SNR the optimal receiver's performance is found for turned off interference suppression.