SUMMARY: PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow. AVAILABILITY AND IMPLEMENTATION: PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/.

In this lightning talk we will describe the Research Software Directory; a content management system that is tailored to research software with the goal of enabling a qualitative assessment of software impact and improving software findability.

We present a small extension to Haskell called the Key monad. With the Key monad, unique keys of different types can be created and can be tested for equality. When two keys are equal, we also obtain a concrete proof that their types are equal. This gives us a form of dynamic typing, without the need for Typeable constraints. We show that our extension allows us to safely do things we could not otherwise do: it allows us to implement the ST monad (inefficiently), to implement an embedded form of arrow notation, and to translate parametric HOAS to typed de Bruijn indices, among others. Although strongly related to the ST monad, the Key monad is simpler and might be easier to prove safe. We do not provide such a proof of the safety of the Key monad, but we note that, surprisingly, a full proof of the safety of the ST monad also remains elusive to this day. Hence, another reason for studying the Key monad is that a safety proof for it might be a stepping stone towards a safety proof of the ST monad.

We present a new interface for practical Functional Reactive Programming (FRP) that (1) is close in spirit to the original FRP ideas, (2) does not have the original space-leak problems, without using arrows or advanced types, and (3) provides a simple and expressive way for performing IO actions from FRP code. We also provide a denotational semantics for this new interface, and a technique (using Kripke logical relations) for reasoning about which FRP functions may "forget their past", i.e. which functions do not have an inherent space-leak. Finally, we show how we have implemented this interface as a Haskell library called FRPNow.

A series of list appends or monadic binds for many monads performs algorithmically worse when left-associated. Continuation-passing style (CPS) is well-known to cure this severe dependence of performance on the association pattern. The advantage of CPS dwindles or disappears if we have to examine or modify the intermediate result of a series of appends or binds, before continuing the series. Such examination is frequently needed, for example, to control search in non-determinism monads.

The well-known Reingold–Tilford algorithm produces tidy-layered drawings of trees: drawings where all nodes at the same depth are vertically aligned. However, when nodes have varying heights, layered drawing may use more vertical space than necessary. A non-layered drawing of a tree places children at a fixed distance from the parent, thereby giving a more vertically compact drawing. Moreover, non-layered drawings can also be used to draw trees where the vertical position of each node is given, by adding dummy nodes. In this paper, we present the first linear-time algorithm for producing non-layered drawings. Our algorithm is a modification of the Reingold–Tilford algorithm, but the original complexity proof of the Reingold–Tilford algorithm uses an invariant that does not hold for the non-layered case. We give an alternative proof of the algorithm and its extension to non-layered drawings. To improve drawings of trees of unbounded degree, extensions to the Reingold–Tilford algorithm have been proposed. These extensions also work in the non-layered case, but we show that they then cause a O(n2) run-time. We then propose a modification to these extensions that restores the O(n) run-time. Copyright © 2013 John Wiley & Sons, Ltd.

Functional Reactive Programming (FRP) is a way to program reactive systems in functional style, eliminating many of the problems that arise from imperative techniques. In this paper, we present an alternative FRP formulation that is based on the notion of a reactive computation: a monadic computation which may require the occurrence of external events to continue. A signal computation is a reactive computation that may also emit values. In contrast to signals in other FRP formulations, signal computations can end, leading to a monadic interface for sequencing signal phases. This interface has several advantages: routing is implicit, sequencing signal phases is easier and more intuitive than when using the switching combinators found in other FRP approaches, and dynamic lists require much less boilerplate code. In other FRP approaches, either the entire FRP expression is re-evaluated on each external stimulus, or impure techniques are used to prevent redundant re-computations. We show how Monadic FRP can be implemented straightforwardly in a purely functional way while preventing redundant re-computations.