The 2015 Bioinformatics Open Source Conference (BOSC 2015).

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

Bayesian Model Averaging in the M-Open Framework

This chapter presents a model averaging approach in the M-open setting using sample re-use methods to approximate the predictive distribution of future observations. It first reviews the standard M-closed Bayesian Model Averaging approach and decision-theoretic methods for producing inferences and decisions. It then reviews model selection from the M-complete and M-open perspectives, before formulating a Bayesian solution to model averaging in the M-open perspective. It constructs optimal weights for MOMA:M-open Model Averaging using a decision-theoretic framework, where models are treated as part of the ‘action space’ rather than unknown states of nature. Using ‘incompatible’ retrospective and prospective models for data from a case-control study, the chapter demonstrates that MOMA gives better predictive accuracy than the proxy models. It concludes with open questions and future directions.

Metadaten für Open Educational Resources (OER). Eine Handreichung für die öffentliche Hand, erstellt von der Technischen Informationsbibliothek (TIB)

"Im Zuge der weiteren Verbreitung der Social Media und der internetbasierten Lehre, gewinnen eLearning Inhalte immer mehr an Bedeutung. In den Kontext von eLearning und internetbasierter Lehre gehören auch Open Educational Resources (OER). OER sind digitale Lern- und Lehrmaterialien, die frei für Lehrende und Studierende zugänglich sind und auch frei verbreitet werden dürfen. [...] Um OER auszutauschen, zu finden, zu beschaffen und sie auf einer breiten Basis zugänglich zu machen, insbesondere auch über Suchmaschinen und dadurch verwenden zu können, werden für die jeweiligen Materialien Metadaten benötigt. [...] Um die Frage nach dem Handlungs- und Forschungsbedarf zum Thema Metadaten für Open Educational Resources zu untersuchen, wird zunächst ein Überblick über die momentan bestehenden nationalen und internationalen Metadatenstandards für eLearning Objekte gegeben. [...] Hieraus ergeben sich Empfehlungen, welche Metadaten-Standards für die weitere Nutzung und Förderung geeignet sein könnten. Es werden außerdem die Möglichkeiten der Erstellung eines neuen Metadaten-Standards sowie eines gemeinsamen Portals für OER erörtert. Hierbei wird vor allem auf die zu erwartenden Probleme und die damit verbundenen Anforderungen eingegangen." (DIPF/Orig.)

The open shop scheduling problem with a given sequence of jobs on one machine

The paper considers the open shop scheduling problem to minimize the make-span, provided that one of the machines has to process the jobs according to a given sequence. We show that in the preemptive case the problem is polynomially solvable for an arbitrary number of machines. If preemption is not allowed, the problem is NP-hard in the strong sense if the number of machines is variable, and is NP-hard in the ordinary sense in the case of two machines. For the latter case we give a heuristic algorithm that runs in linear time and produces a schedule with the makespan that is at most 5/4 times the optimal value. We also show that the two-machine problem in the nonpreemptive case is solvable in pseudopolynomial time by a dynamic programming algorithm, and that the algorithm can be converted into a fully polynomial approximation scheme. © 1998 John Wiley & Sons, Inc. Naval Research Logistics 45: 705–731, 1998

A greedy open shop heuristic with job priorities

The paper presents an improved version of the greedy open shop approximation algorithm with pre-ordering of jobs. It is shown that the algorithm compares favorably with the greedy algorithm with no pre-ordering by reducing either its absolute or relative error. In the case of three machines, the new algorithm creates a schedule with the makespan that is at most 3/2 times the optimal value.

A 3/2 algorithm for two-machine open shop with route-dependent processing times

This paper considers the problem of minimizing the schedule length of a two-machine shop in which not only can a job be assigned any of the two possible routes, but also the processing times depend on the chosen route. This problem is known to be NP-hard. We describe a simple approximation algorithm that guarantees a worst-case performance ratio of 2. We also present some modifications to this algorithm that improve its performance and guarantee a worst-case performance ratio of 3=2.

A polynomial algorithm for the three-machine open shop with a bottleneck machine

The paper considers the three‐machine open shop scheduling problem to minimize themakespan. It is assumed that each job consists of at most two operations, one of which is tobe processed on the bottleneck machine, the same for all jobs. A new lower bound on theoptimal makespan is derived, and a linear‐time algorithm for finding an optimalnon‐preemptive schedule is presented.

Group technology approach to the open shop scheduling problem with batch setup times

This paper studies the problem of scheduling jobs in a two-machine open shop to minimize the makespan. Jobs are grouped into batches and are processed without preemption. A batch setup time on each machine is required before the first job is processed, and when a machine switches from processing a job in some batch to a job of another batch. For this NP-hard problem, we propose a linear-time heuristic algorithm that creates a group technology schedule, in which no batch is split into sub-batches. We demonstrate that our heuristic is a -approximation algorithm. Moreover, we show that no group technology algorithm can guarantee a worst-case performance ratio less than 5/4.

An open shop scheduling problem with a non-bottleneck machine

This paper considers the problem of processing n jobs in a two-machine non-preemptive open shop to minimize the makespan, i.e., the maximum completion time. One of the machines is assumed to be non-bottleneck. It is shown that, unlike its flow shop counterpart, the problem is NP-hard in the ordinary sense. On the other hand, the problem is shown to be solvable by a dynamic programming algorithm that requires pseudopolynomial time. The latter algorithm can be converted into a fully polynomial approximation scheme that runs in time. An O(n log n) approximation algorithm is also designed whi finds a schedule with makespan at most 5/4 times the optimal value, and this bound is tight.

Two-machine open shop scheduling with special transportation times

The paper considers a problem of scheduling n jobs in a two-machine open shop to minimise the makespan, provided that preemption is not allowed and the interstage transportation times are involved. In general, this problem is known to be NP-hard. We present a linear time algorithm that finds an optimal schedule if no transportation time exceeds the smallest of the processing times. We also describe an algorithm that creates a heuristic solution to the problem with job-independent transportation times. Our algorithm provides a worst-case performance ratio of 8/5 if the transportation time of a job depends on the assigned processing route. The ratio reduces to 3/2 if all transportation times are equal.

A heuristic for the two-machine open-shop scheduling problem with transportation times

The paper considers a problem of scheduling n jobs in a two-machine open shop to minimize the makespan, provided that preemption is not allowed and the interstage transportation times are involved. This problem is known to be unary NP-hard. We present an algorithm that requires O (n log n) time and provides a worst-case performance ratio of 3/2.

Scheduling batches with sequential job processing for two-machine flow and open shops

In this paper, we study a problem of scheduling and batching on two machines in a flow-shop and open-shop environment. Each machine processes operations in batches, and the processing time of a batch is the sum of the processing times of the operations in that batch. A setup time, which depends only on the machine, is required before a batch is processed on a machine, and all jobs in a batch remain at the machine until the entire batch is processed. The aim is to make batching and sequencing decisions, which specify a partition of the jobs into batches on each machine, and a processing order of the batches on each machine, respectively, so that the makespan is minimized. The flow-shop problem is shown to be strongly NP-hard. We demonstrate that there is an optimal solution with the same batches on the two machines; we refer to these as consistent batches. A heuristic is developed that selects the best schedule among several with one, two, or three consistent batches, and is shown to have a worst-case performance ratio of 4/3. For the open-shop, we show that the problem is NP-hard in the ordinary sense. By proving the existence of an optimal solution with one, two or three consistent batches, a close relationship is established with the problem of scheduling two or three identical parallel machines to minimize the makespan. This allows a pseudo-polynomial algorithm to be derived, and various heuristic methods to be suggested.

Two-machine open shop scheduling with an availability constraint

We study a two-machine open shop scheduling problem, in which one machine is not available for processing during a given time interval. The objective is to minimize the makespan. We show that the problem is NP-hard and present an approximation algorithm with a worst-case ratio of 4/3.

Two-stage open shop scheduling with a bottleneck machine

It is known that for the open shop scheduling problem to minimize the makespan there exists no polynomial-time heuristic algorithm that guarantees a worst-case performance ratio better than 5/4, unless P6≠NP. However, this result holds only if the instance of the problem contains jobs consisting of at least three operations. This paper considers the open shop scheduling problem, provided that each job consists of at most two operations, one of which is to be processed on one of the m⩾2 machines, while the other operation must be performed on the bottleneck machine, the same for all jobs. For this NP-hard problem we present a heuristic algorithm and show that its worst-case performance ratio is 5/4.