Process mining techniques are able to extract knowledge from event logs commonly available in today’s information systems. These techniques provide new means to discover, monitor, and improve processes in a variety of application domains. There are two main drivers for the growing interest in process mining. On the one hand, more and more events are being recorded, thus, providing detailed information about the history of processes. On the other hand, there is a need to improve and support business processes in competitive and rapidly changing environments. This manifesto is created by the IEEE Task Force on Process Mining and aims to promote the topic of process mining. Moreover, by defining a set of guiding principles and listing important challenges, this manifesto hopes to serve as a guide for software developers, scientists, consultants, business managers, and end-users. The goal is to increase the maturity of process mining as a new tool to improve the (re)design, control, and support of operational business processes

The Arabidopsis seed coat epidermis undergoes a complex process of differentiation that includes the biosynthesis and secretion of large quantities of pectinaceous mucilage, cytoplasmic rearrangement, and secondary cell wall biosynthesis. Mutations in MUM4 (MUCILAGE-MODIFIED4) lead to a decrease in seed coat mucilage and incomplete cytoplasmic rearrangement. We show that MUM4 encodes a putative NDP-l-rhamnose synthase, an enzyme required for the synthesis of the pectin rhamnogalacturonan I, the major component of Arabidopsis mucilage. This result suggests that the synthesis of monosaccharide substrates is a limiting factor in the biosynthesis of pectinaceous seed coat mucilage. In addition, the reduced cytoplasmic rearrangement observed in the absence of a key enzyme in pectin biosynthesis in mum4 mutants establishes a causal link between mucilage production and cellular morphogenesis. The cellular phenotype seen in mum4 mutants is similar to that of several transcription factors (AP2 [APETALA2], TTG1 [TRANSPARENT TESTA GLABRA1], TTG2 MYB61, and GL2 [GLABRA2]). Expression studies suggest that MUM4 is developmentally regulated in the seed coat by AP2, TTG1, and GL2, whereas TTG2 and MYB61 appear to be regulating mucilage production through alternate pathway(s). Our results provide a framework for the regulation of mucilage production and secretory cell differentiation.The mature seed coat, in addition to forming a protective layer around the embryo, can play roles in such processes as seed dispersal and germination. One adaptation believed to act in these processes is the production of mucilage in the epidermal cells of the seed coat. This specialization, known as myxospermy, is found in many families, including the Brassicaceae, Solanaceae, Linaceae, and Plantaginaceae (Grubert, 1981; Boesewinkel and Bouman, 1995). Seed imbibition in these plants leads to the formation of a gel capsule around the seed that is thought to aid hydration and/or dispersal. Mucilage consists of pectins, a heterogeneous group of acidic polysaccharides that form a gel-like matrix. In the primary cell wall, pectins form the matrix in which cellulose microfibrils and hemicelluloses are embedded. Key pectins include homo-GalUA (HGA) and rhamnogalacturonan I (RGI). HGA consists of an unbranched chain of ␣-1,4-linked GalUA residues whose carboxyl groups may be modified through methyl-esterification. RGI has a backbone of alternating ␣-1,2-linked Rha and ␣-1,4-linked GalUA residues, with sugar side chains attached on varying numbers of Rha residues. Both HGA and RGI are believed to be synthesized in the Golgi apparatus through the activities of glycosyltransferases using nucleotide sugars imported from the cytoplasm (for review, see Ridley et al., 2001). Chemical analysis of Arabidopsis mucilage has shown that it is composed largely of ␣-1,2 linked Rha and ␣-1,4 linked GalUA, suggesting that it is comprised primarily of RGI (Penfield et al., 2001). Immunofluorescence studies of mucilage have demonstrated the presence of methylesterified HGA ...

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The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, pre-processing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.

In Arabidopsis, fertilization induces the epidermal cells of the outer ovule integument to differentiate into a specialized seed coat cell type producing extracellular pectinaceous mucilage and a volcano-shaped secondary cell wall. Differentiation involves a regulated series of cytological events including growth, cytoplasmic rearrangement, mucilage synthesis, and secondary cell wall production. We have tested the potential of Arabidopsis seed coat epidermal cells as a model system for the genetic analysis of these processes. A screen for mutants defective in seed mucilage identified five novel genes (MUCILAGE-MODIFIED [MUM]1-5). The seed coat development of these mutants, and that of three previously identified ones (TRANSPARENT TESTA GLABRA1, GLABRA2, and APETALA2) were characterized. Our results show that the genes identified define several events in seed coat differentiation. Although APETALA2 is needed for differentiation of both outer layers of the seed coat, TRANSPARENT TESTA GLABRA1, GLABRA2, and MUM4 are required for complete mucilage synthesis and cytoplasmic rearrangement. MUM3 and MUM5 may be involved in the regulation of mucilage composition, whereas MUM1 and MUM2 appear to play novel roles in post-synthesis cell wall modifications necessary for mucilage extrusion.Fertilization of the angiosperm ovule not only results in the development of the embryo and endosperm, but also initiates differentiation of the ovule integuments to form the seed coat. The seed coat consists of multiple specialized cell layers that play important roles in embryo protection and the regulation of germination. One specialization is known as myxospermy, a property of epidermal cells whereby they produce large quantities of pectic polysaccharide (mucilage; Frey-Wyssling, 1976; Grubert, 1981; Boesewinkel and Bouman, 1995). Myxospermy is commonly found in species of the Brassicaceae, Solanaceae, Linaceae, and Plantaginaceae, where mucilage forms a gel-like capsule surrounding the seed upon imbibition. Proposed roles for mucilage include facilitating seed hydration and/or dispersal. Mucilages are also found in the root cap and transmitting tract (Frey-Wyssling, 1976; Esau, 1977), where they foster root tip and pollen tube growth, respectively.Mucilages are largely composed of pectins, a heterogeneous group of complex, acidic polysaccharides that also comprise the majority of the plant cell wall matrix. Dicotyledonous pectins largely consist of poly-GalUA (PGA) and rhamnogalacturonan I (RG I; Brett and Waldron, 1990; Carpita and Gibeaut, 1993; Cosgrove, 1997). PGA is composed of an unbranched chain of ␣1,4-linked GalUA residues, whereas RG I is a highly branched polysaccharide with a backbone of alternating ␣1,4-linked GalUA and ␣1,2-linked rhamnose (Rha), with sugar side chains attached to the Rha residues (Brett and Waldron, 1990). The degree of gelling of pectins is largely dependent on ionic bonding between PGA molecules and free divalent calcium. Thus, cell wall fluidity is affected by the degree of methyl esterification of...