A Bioinformatician's Guide to Metagenomics

Summary: As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.     

A Guide to Scientific Crowdfunding

Crowdfunding represents an attractive new option for funding research projects, especially for students and early-career scientists or in the absence of governmental aid in some countries. The number of successful science-related crowdfunding campaigns is growing, which demonstrates the public’s willingness to support and participate in scientific projects. Putting together a crowdfunding campaign is not trivial, however, so here is a guide to help you make yours a success.     

Organization of Clinical Trial on National Scale: Management of Early Cancer of the Breast

From a study of the organization of a national clinical trial on the management of early cancer of the breast in women there appear to be overwhelming advantages in studying large numbers of patients. To this end centres abroad have been encouraged to join. All the evidence at present suggests that it is feasible to organize a study on this scale, that the documentation and follow-up are accurate, and that the enthusiasm of the participants can be successfully fostered and maintained.     

Myasthenia Gravis: Brief Guide to Diagnosis and Management

Physicians should consider the possibility of myasthenia gravis in patients complaining of fluctuating muscle weakness and easy fatigability. The disorder may occur in either sex at any age. Repeated measurements of multiple muscle groups and functions to include baseline strength and response to a control as well as anticholinesterase drugs are desirable in reaching a diagnosis. Appropriate doses of anticholinesterase medication reduce weakness and fatigability in most patients. Selected patients may benefit from thymectomy. Patients in crisis failing to respond to anticholinesterase drugs, having difficulty maintaining a patent airway or adequate respiratory exchange are best managed by prompt tracheostomy using a cuffed tube, with adequate tracheobronchial toilet and mechanical respiratory assistance.