Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa.

Although most cases are identified at a late stage, breast cancer is the most public malignancy amongst women globally. However, mammography for the analysis of breast cancer is not routinely available at all general hospitals. Prolonging the period between detection and treatment for breast cancer may raise the likelihood of proliferating the disease. To speed up the process of diagnosing breast cancer and lower the mortality rate, a computerized method based on machine learning was created. The purpose of this investigation was to enhance the investigative accuracy of machine-learning algorithms for breast cancer diagnosis. The use of machine-learning methods will allow for the classification and prediction of cancer as either benign or malignant. This investigation applies the machine learning algorithms of random forest (RF) and the support vector machine (SVM) with the feature extraction method of linear discriminant analysis (LDA) to the Wisconsin Breast Cancer Dataset. The SVM with LDA and RF with LDA yielded accuracy results of 96.4% and 95.6% respectively. This research has useful applications in the medical field, while it enhances the efficiency and precision of a diagnostic system. Evidence from this study shows that better prediction is crucial and can benefit from machine learning methods. The results of this study have validated the use of feature extraction for breast cancer prediction when compared to the existing literature.

Purpose: Breast cancer remains a serious public health problem that results in the loss of lives among women. However, early detection of its signs increases treatment options and the likelihood of cure. Although mammography has been established to be a proven technique of examining symptoms of cancer in mammograms, the manual observation by radiologists is demanding and often prone to diagnostic errors. Therefore, computer aided diagnosis (CADx) systems could be a viable alternative that could facilitate and ease cancer diagnosis process; hence this study. Methodology: The inputs to the proposed model are raw mammograms downloaded from the Mammographic Image Analysis Society database. Prior to the classification, the raw mammograms were preprocessed. Then, gray level co-occurrence matrix was used to extract fifteen textural features from the mammograms at four different angular directions: θ={0°, 45°, 90°, 135°}, and two distances: D={1,2}. Afterwards, a two-stage support vector machine was used to classify the mammograms as normal, benign and malignant. Results: All of the 37 normal images used as test data were classified as normal (no false positive) and all 41 abnormal images were correctly classified to be abnormal (no false negative), meaning that the sensitivity and specificity of the model in detecting abnormality is 100%. After the detection of abnormality, the system further classified the abnormality on the mammograms to be either “benign” or “malignant”. Out of 23 benign images, 21 were truly classified as benign. Also, out of 18 malignant images, 17 were truly classified to be malignant. From these findings, the sensitivity, specificity, positive predictive value, and negative predictive value of the system are 94.4%, 91.3%, 89.5%, and 95.5%, respectively. Conclusion: This article has further affirmed the prowess of automated CADx systems as a viable tool that could facilitate breast cancer diagnosis by radiologists.

The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so. Many programs have been developed to boost the technical and computational skills of scientists working in low to medium income countries (LMIC), who often struggle to remain competitive with their peers in more developed parts of the world. Typically, these programs rely on intensive workshops where students acquire and exercise these skills under the supervision of experienced trainers. However, when trainees return to their home institutions, even after extensive exposure to state of the art techniques, they often find it difficult to put the skills they have acquired into practice and to establish themselves as fully independent practitioners. We have attempted to build a framework through which teams of scientists in African research groups can demonstrate that they have acquired the necessary skills to analyze different types of genomic datasets. Three teams of scientists who have successfully submitted to this assessment exercise report their positive experiences. Many potential participants have so far declined the opportunity, and we discuss the reasons for their reluctance as well as possible ways to facilitate their engagement and provide them with incentives. We argue that assessments such as this could be part of any program aiming to develop technical skills in scientists wishing to support genomic research programs.