Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features.

Cell signaling dynamics and transcriptional regulatory activities are variable within specific cell types responding to an identical stimulus. In addition to studying the network interactions, there is much interest in utilizing single cell scale data to elucidate the non-random aspects of the variability involved in cellular decision making. Previous studies have considered the information transfer between the signaling and transcriptional domains based on an instantaneous relationship between the molecular activities. These studies predict a limited binary on/off encoding mechanism which underestimates the complexity of biological information processing, and hence the utility of single cell resolution data. Here we pursue a novel strategy that reformulates the information transfer problem as involving dynamic features of signaling rather than molecular abundances. We pursue a computational approach to test if and how the transcriptional regulatory activity patterns can be informative of the temporal history of signaling. Our analysis reveals (1) the dynamic features of signaling that significantly alter transcriptional regulatory patterns (encoding), and (2) the temporal history of signaling that can be inferred from single cell scale snapshots of transcriptional activity (decoding). Immediate early gene expression patterns were informative of signaling peak retention kinetics, whereas transcription factor activity patterns were informative of activation and deactivation kinetics of signaling. Moreover, the information processing aspects varied across the network, with each component encoding a selective subset of the dynamic signaling features. We developed novel sensitivity and information transfer maps to unravel the dynamic multiplexing of signaling features at each of these network components. Unsupervised clustering of the maps revealed two groups that aligned with network motifs distinguished by transcriptional feedforward vs feedback interactions. Our new computational methodology impacts the single cell scale experiments by identifying downstream snapshot measures required for inferring specific dynamical features of upstream signals involved in the regulation of cellular responses

The challenges of staying together while moving fast

We report on the results of an empirical study conducted with 35 experienced software developers from 22 high-tech companies, including Google, Facebook, Microsoft, Intel, and others. The goal of the study was to elicit challenges that these developers face, potential solutions that they envision to these challenges, and research initiatives that they think would deliver useful results. Challenges identified by the majority of the study participants relate to the collaborative nature of the work: the availability and discoverability of information, communication, collaborative planning and integration with work of others. Almost all participants also addressed the advantages and disadvantages of the current "fast to the market" trend, and the toll it takes on the quality of the software that they are able to deliver and on their professional and personal satisfaction as software engineers. We describe in depth the identified challenges, supporting our findings with explicit quotes from the study participants. We also put these findings in context of work done by the software engineering community and outline a roadmap for possible future research initiatives

Discovering Software Process Deviations Using Visualizations

Peer reviewe

Some Findings Concerning Requirements in Agile Methodologies

gile methods have appeared as an attractive alternative to conventional methodologies. These methods try to reduce the time to market and, indirectly, the cost of the product through flexible development and deep customer involvement. The processes related to requirements have been extensively studied in literature, in most cases in the frame of conventional methods. However, conclusions of conventional methodologies could not be necessarily valid for Agile; in some issues, conventional and Agile processes are radically different. As recent surveys report, inadequate project requirements is one of the most conflictive issues in agile approaches and better understanding about this is needed. This paper describes some findings concerning requirements activities in a project developed under an agile methodology. The project intended to evolve an existing product and, therefore, some background information was available. The major difficulties encountered were related to non-functional needs and management of requirements dependencies

Key Challenges in Agile Requirements Engineering

Agile Software Development (ASD) is becoming more popular in all fields of industry. For an agile transformation, organizations need to continuously improve their established approaches to Requirements Engineering (RE) as well as their approaches to software development. This is accompanied by some chal‐lenges in terms of agile RE. The main objective of this paper is to identify the most important challenges in agile RE industry has to face today. Therefore, we conducted an iterative expert judgement process with 26 experts in the field of ASD, comprising three complementary rounds. In sum, we identified 20 challenges in three rounds. Six of these challenges are defined as key challenges. Based on the results, we provide options for dealing with those key challenges by means of agile techniques and tools. The results show that the identified challenges are often not limited to ASD, but they rather refer to software development in general. Therefore, we can conclude that organ‐izations still struggle with agile transition and understanding agile values, in particular, in terms of stakeholder and user involvement.Ministerio de Economía y Competitividad TIN2013-46928-C3-3-RMinisterio de Economía y Competitividad TIN2016-76956-C3-2-RMinisterio de Economía y Competitividad TIN2015-71938-RED

A study of the Scrum Master’s role

Scrum is an increasingly common approach to software development adopted by organizations around the world. However, as organizations transition from traditional plan-driven development to agile development with Scrum, the question arises as to which Scrum role (Product Owner, Scrum Master, or Scrum Team Member) corresponds to a Project Manager, or conversely which Scrum role should the Project Managers adopt? In an attempt to answer this question, we adopted a mixed-method research approach comprising a systematic literature review and embedded case study of a commercial software development team. Our research has identified activities that comprise the Scrum Master role, and which additional roles are actually performed by Scrum Masters in practice. We found nine activities that are performed by Scrum Masters. In addition, we found that Scrum Masters also perform other roles, most importantly as Project Managers. This latter situation results in tension and conflict of interest that could have a negative impact on the performance of the team as a whole. These results point to the need to re-assess the role of Project Managers in organizations that adopt Scrum as a development approach. We hypothesize that it might be better for Project Managers to become Product Owners, as aspects of this latter role are more consistent with the traditional responsibilities of a Project Manager

Historical roots of Agile methods: where did “Agile thinking” come from?

The appearance of Agile methods has been the most noticeable change to software process thinking in the last fifteen years [16], but in fact many of the “Agile ideas” have been around since 70’s or even before. Many studies and reviews have been conducted about Agile methods which ascribe their emergence as a reaction against traditional methods. In this paper, we argue that although Agile methods are new as a whole, they have strong roots in the history of software engineering. In addition to the iterative and incremental approaches that have been in use since 1957 [21], people who criticised the traditional methods suggested alternative approaches which were actually Agile ideas such as the response to change, customer involvement, and working software over documentation. The authors of this paper believe that education about the history of Agile thinking will help to develop better understanding as well as promoting the use of Agile methods. We therefore present and discuss the reasons behind the development and introduction of Agile methods, as a reaction to traditional methods, as a result of people's experience, and in particular focusing on reusing ideas from histor

From Empowerment Dynamics to Team Adaptability: Exploring and Conceptualizing the Continuous Agile Team Innovation Process

To foster their innovation teams’ adaptability, organizations are increasingly relying on agile teams. While research on the adoption of agile methods and practices has grown tremendously in the past decade, little is currently known about the human side of agile teams and how it contributes toward the emergence of adaptability. While the Agile Manifesto states that individuals and interactions are more important for agile product development than tools and processes, research on how these interactions unfold is still in its infancy. To shed light on the human side of adaptability, 44 semi‐structured, in‐depth interviews were conducted with team members and leaders from various teams at three organizations (i.e., two German and one multinational European firm). The inductive analysis identified empowerment as a focal human factor for adaptability emergence. A model of the continuous agile team innovation process is developed and uncovers the importance of dynamic empowerment states and their temporary equilibria for team adaptability. The underlying findings demonstrate that empowerment is not a static state, but rather emerges through the interactions between various actors. Specifically, the team and its leader engage in both empowerment‐enhancing and empowerment‐reducing activities. These activities are further influenced by the agile team’s immediate context: Two‐fold customer influences, that is, supporting and hindering empowerment interactions, and the organizational environment, that is, undergoing an agile transformation and supportive top management behaviors, play an important role in affecting the empowerment dynamics that result in team adaptability. As such, this study contributes to the innovation and management literatures by revealing the dynamic role of the empowerment and adaptability constructs for agile innovation processes and the importance of various actors and the organizational environment for fostering adaptability. Practical insights are offered to management, teams, and team members on how to create conditions for empowerment dynamics and consequently adaptability to unfold